Submission: SymbiotaR2

[akoontz11]

Submitting Author: Austin Koontz (@akoontz11 )
Repository: https://github.com/pearselab/SymbiotaR2
Version submitted: 0.0.1
Editor: @noamross
Reviewers: @bpbond, @sckott

Due date for @bpbond: 2020-06-25

Due date for @sckott: 2020-08-31
Archive: TBD
Version accepted: TBD

---

• Paste the full DESCRIPTION file inside a code block below:

Package: SymbiotaR2
Type: Package
Title: Downloading data from Symbiota2 portals into R
Version: 0.0-1
Authors@R: c(person("Austin", "Koontz", email = "austin.koontz@usu.edu", role = c("aut", "cre")),
    person("William D.", "Pearse", email = "will.pearse@gmail.com", role ="aut", comment=c(ORCID="0000-0002-6241-3164")))
Maintainer: Austin Koontz <austin.koontz@usu.edu>
Description: Download data from Symbiota2 portals using Symbiota's
    API. Covers the Checklists, Collections, Crowdsource, Exsiccati,
    Glossary, ImageProcessor, Key, Media, Occurrence, Reference, Taxa,
    Traits, and UserRoles API families. Each Symbiota2 portal owner
    can load their own plugins (and modified code), and so this
    package may not cover every possible API endpoint from a given
    Symbiota2 instance.
License: MIT + file LICENSE
URL: https://github.com/pearselab/SymbiotaR2
BugReports: https://github.com/pearselab/SymbiotaR2/issues
VignetteBuilder: knitr
LazyLoad: yes
Suggests:
    knitr (>= 1.23),
    testthat (>= 2.0.0),
    vcr (>= 0.3.0)	
Imports:
    httr (>= 1.0.0),
    xml2 (>= 1.2.0),
    rjson (>= 0.2.20),
    fs (>= 1.2.6)
Encoding: UTF-8
RoxygenNote: 7.0.2

Scope

• Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):

  • data retrieval
  • data extraction
  • database access
  • data munging
  • data deposition
  • workflow automataion
  • version control
  • citation management and bibliometrics
  • scientific software wrappers
  • database software bindings
  • geospatial data
  • text analysis

• Explain how and why the package falls under these categories (briefly, 1-2 sentences):

The primary purpose of SymbiotaR2 is to allow users to pull objects from the specified Symbiota2 database portal into an R environment. It does this by wrapping each of the default API calls made available on the Symbiota2 portal of interest.

• Who is the target audience and what are scientific applications of this package?

The target audiences includes anyone interested in using R to analyze biological specimen data made available through the Symbiota2 content management system. Potential scientific applications include comparing biological trait data between different lineages, analyzing phenological data, and biodiversity research generally.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?

No R packages have been developed for the updated code structure provided by Symbiota2.

• If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

Technical checks

Confirm each of the following by checking the box.

• I have read the guide for authors and rOpenSci packaging guide.

This package:

• does not violate the Terms of Service of any service it interacts with.
• has a CRAN and OSI accepted license.
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, including reporting of test coverage using services such as Travis CI, Coveralls and/or CodeCov.

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• Do you intend for this package to go on CRAN?
• Do you intend for this package to go on Bioconductor?
• Do you wish to automatically submit to the Journal of Open Source Software? If so:

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• The package has an obvious research application according to JOSS's definition.
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MEE Options

• The package is novel and will be of interest to the broad readership of the journal.
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Code of conduct

• I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

[akoontz11]

Tagging @willpearse as a contributing author of this package as well.

[noamross]

Editor checks:

• Fit: The package meets criteria for fit and overlap
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
• License: The package has a CRAN or OSI accepted license
• Repository: The repository link resolves correctly
• Archive (JOSS only, may be post-review): The repository DOI resolves correctly
• Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

---

Editor comments

Thank you for your submission @akoontz11!

Here is output from goodpractice::gp(). Your test coverage is good, and the >80 lines are mostly just due to indention conventions. I note that you use sapply() in basically the same way all over the package and it might make sense to make a small utility function replacing this use that uses vapply(), which might also make code clearer. I also note that the documentation can be a little terse; README or other documentation might go into more detail, as to the the nature of Symbiota data and data types following the principle of mutiple points of entry. None of these things require holding up review; I am seeking reviewers and will ask them to evaluate these observations.

── GP SymbiotaR2 ────────────────────────────

It is good practice to

  ✖ write unit tests for all functions, and all package code
    in general. 87% of code lines are covered by test cases.

    R/Defaults.R:28:NA
    R/Defaults.R:31:NA
    R/Defaults.R:32:NA
    R/Defaults.R:33:NA
    R/Defaults.R:34:NA
    ... and 57 more lines

  ✖ avoid long code lines, it is bad for readability. Also,
    many people prefer editor windows that are about 80 characters
    wide. Try make your lines shorter than 80 characters

    R/Checklists.R:3:1
    R/Checklists.R:10:1
    R/Checklists.R:11:1
    R/Checklists.R:21:1
    R/Checklists.R:43:1
    ... and 99 more lines

  ✖ avoid sapply(), it is not type safe. It might return a
    vector, or a list, depending on the input data. Consider using
    vapply() instead.

    R/Checklists.R:24:13
    R/Checklists.R:32:20
    R/Checklists.R:70:17
    R/Checklists.R:90:13
    R/Checklists.R:98:20
    ... and 14 more lines

---

Reviewers: @abarner @bpbond
Due date: 2020-06-25

[willpearse]

Brilliant, thank you Dr Ross! If it's OK with you, can we wait until after the reviews are back in to address your `sapply` and documentation suggestions? I imagine there will be other comments and it might be easier to address everything at once.

…

[noamross]

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[annakrystalli]

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In the interest of reducing load on reviewers and editors as we manage the
COVID-19 crisis, rOpenSci new submissions for software peer review are paused.

In this period new submissions will not be handled, nor new reviewers assigned.
Reviews and responses to reviews will be handled on a 'best effort' basis, but
no follow-up reminders will be sent.
Other rOpenSci community activities continue.

Please check back here again after 25 May when we will be announcing plans to slowly start back up.

We express our continued great
appreciation for the work of our authors and reviewers. Stay healthy and take
care of one other.

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[noamross]

Hello @akoontz11 and @willpearse, we're starting up review activities again so I'll be seeking reviewers now, but I wanted to check in and see if there are any developments. Anything I should know about updates to the package or your schedule? Thanks for your patience on this!

[willpearse]

Thanks, but there have been no changes. No worries about the delay.

…

[noamross]

My apologies this is taking a while. I've been digging through the various Symbiota portal organizations looking for people who use it who may be reviewers. Do you know any Symbiota users/administrators to suggest as reviewers?

[willpearse]

Thanks Noam. I do know some, but I worry that suggesting one of my friends would be a bit unethical! Have you found this list ( http://symbiota.org/docs/symbiota-introduction/active-symbiota-projects/)? I should add that many herbarium managers are not R developers, and so they might be unwilling to review an R package (they're often taxonomic experts). Another option might be someone who has spent a lot of time working with natural history collection data; an example would be Emily Meinke (although we shared a post-doc advisor; https://emilykmeineke.com/).

…

[noamross]

Thanks Will. I've found two reviewers. Thank you @abarner and @bpbond for agreeing to review! Due date is 2020-06-25