Submission: rcites

[JonasGeschke]

Summary

• What does this package do? (explain in 50 words or less):
  With rcites we provide an R client to access to the Speciesplus database. We provide functions to 1. access the Speciesplus taxon concept, and thereafter 2. get a species' legislation status, both from CITES and from the European Union, 3. get a species' country-wise distribution range, as listed in Speciesplus, and 4. get the references on which a Speciesplus listing is based.

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

Package: rcites
Type: Package
Title: R Interface to the Species+ Database
Version: 0.1.0
Authors@R: c(person("Jonas", "Geschke", role = c("aut"), email = "jonas.e.geschke@gmail.com", comment = c(ORCID = "0000-0002-5654-9313")),
  person("Kevin", "Cazelles", role = c("aut", "cre"), email = "kevin.cazelles@gmail.com", comment = c(ORCID = "0000-0001-6619-9874")),
  person("Ignasi", "Bartomeus", role = c("aut"), comment = c(ORCID = "0000-0001-7893-4389")),
  person("Jonathan", "Goldenberg", role = c("ctb")),
  person("Marie-Bé", "Leduc", role = c("ctb")),
  person("Yasmine", "Verzelen", role = c("ctb")))
Description: A programmatic interface to the Species+ <https://speciesplus.net/> database via the Species+/CITES Checklist API <https://api.speciesplus.net/>.
URL: https://ibartomeus.github.io/rcites/, https://github.com/ibartomeus/rcites
BugReports: https://github.com/ibartomeus/rcites/issues
License: MIT + file LICENSE
Depends:
  R (>= 3.1.0)
Imports:
  httr,
  data.table,
  methods
Encoding: UTF-8
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown, testthat, rworldmap
VignetteBuilder: knitr

• URL for the package (the development repository, not a stylized html page):
  https://github.com/ibartomeus/rcites

• Please indicate which category or categories from our package fit policies this package falls under *and why(? (e.g., data retrieval, reproducibility. If you are unsure, we suggest you make a pre-submission inquiry.):
  Database access, because the package gives access to the Species+/CITES Checklist API

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

• 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

•   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.

Requirements

Confirm each of the following by checking the box. 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.
• I agree to abide by ROpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

Publication options

• Do you intend for this package to go on CRAN?
• Do you wish to automatically submit to the Journal of Open Source Software? If so:
  • The package has an obvious research application according to JOSS's definition.
  • The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
  • The package is deposited in a long-term repository with the DOI:
  • (Do not submit your package separately to JOSS)
• Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:
  • The package is novel and will be of interest to the broad readership of the journal.
  • The manuscript describing the package is no longer than 3000 words.
  • You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see MEE's Policy on Publishing Code)
  • (Scope: Do consider MEE's Aims and Scope for your manuscript. We make no gaurantee that your manuscript willl be within MEE scope.)
  • (Although not required, we strongly recommend having a full manuscript prepared when you submit here.)
  • (Please do not submit your package separately to Methods in Ecology and Evolution)

Detail

• Does R CMD check (or devtools::check()) succeed? Paste and describe any errors or warnings:

• Does the package conform to rOpenSci packaging guidelines? Please describe any exceptions:

• If this is a resubmission following rejection, please explain the change in circumstances:

• If possible, please provide recommendations of reviewers - those with experience with similar packages and/or likely users of your package - and their GitHub user names:
  https://github.com/karthik
  https://github.com/geanders

[sckott]

hi @JonasGeschke Thanks for your submission.

I have a clarifying question. What is the relationship of Species+/CITES to IUCN Red List, if any? Does it contain any overlapping information/data?

(p.s. you didn't check Do you intend for this package to go on CRAN? - i think you're pkg is already on CRAN, so go ahead and check that)

[JonasGeschke]

Hi @sckott thanks for your quick message.

There is no relationship between the IUCN Red List and the CITES Speciesplus database. The IUCN Red List contains data about the conservation/endangerment status of species; the CITES Speciesplus database contains data about the (illegal) trade status of endangered species, so it goes beyond the Red List. Actually, the Speciesplus database also contains data about the protection status of species under the Convention on Migrating Species (CMS), but the API so far only allows access to the CITES legislation status information.

Regarding the Do you intend for this package to go on CRAN? question thats right. By mistake, we already submitted the package to CRAN before having it reviewed via ROpenSci. So we dont intend the package to go on CRAN, as it already is on CRAN. Thus, we are looking forward to the reviewing process and how big the first update of the package on CRAN will be.

[sckott]

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

Thanks for your submission @JonasGeschke !

Here's the output from goodpractice. If you haven't used goodpractice it's an R package that checks a number of things with another package - most of which we agree with and want authors to follow. You don't need to address these now, it's info for reviewers to use to get started. There's very little in the report below, which is a good thing!

── GP rcites ──────────

It is good practice to

  ✖ 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/sppplus_simplify.R:29:1
    R/sppplus_simplify.R:32:1
    R/sppplus_simplify.R:50:1
    R/sppplus_taxonconcept.R:35:1
    R/sppplus_taxonconcept.R:48:1
    ... and 30 more lines

Seeking reviewers now 🕐

---

Reviewers:

• @noamross due date 2018-09-07
• @mcsiple due date 2018-09-10

[KevCaz]

@sckott thanks!

Actually, following the guidelines of Ropenscience, we've used goodpractice (that's why we got rid of a sapply()!). Regarding the length of code line issue, I'd be happy to have your feed back: we used tidy_dir() from formatR package with a width.cutoff=80, so, should we reduce the cutoff?

[sckott]

If those lines are already 80 or shorter, then all good. I didn't check them myself. there are definitely exceptions when it's just too cumbersome to do so