submission: rppo

[jdeck88]

Summary

• What does this package do? (explain in 50 words or less):
  The global plant phenology data portal (PPO data portal) is an aggregation of plant phenological observations from USA-NPN, NEON, and PEP725 representing 20 million phenological observations from across North America and Europe. The PPO data portal utilizes the Plant Phenology Ontology to align phenological terms and measurements from the various databases. The rppo R package enables programmatic access to all data contained in the PPO data portal.

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

Package: rppo
Title: R functions to access Plant Phenology Ontology annotated datasets
Date: 2018-03-21
Version: 1.0
Authors@R: as.person(c(
    "John Deck <jdeck88@gmail.com> [aut, cre]", 
    "Brian Stucky <stuckyb@flmnh.ufl.edu> [aut]",
    "Ramona Walls <rwalls@cyverse.org> [aut]",
    "Kjell Bolmgren <Kjell.Bolmgren@slu.se> [aut]",
    "Ellen Denny <ellen@usanpn.org> [aut]",
    "Robert Guralnick <rguralnick@flmnh.ufl.edu> [aut]"
  ))
Maintainer: John Deck <jdeck88@gmail.com>
Description: Access data from the Plant Phenology Ontology data store.
Depends: R (>= 3.4.2)
License: CC0
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1.9000
Imports:
    rjson,
    readr,
    plyr,
    leafletR (>= 0.1-1),
    httr
Suggests: testthat,
    knitr,
    rmarkdown
VignetteBuilder: knitr

• URL for the package (the development repository, not a stylized html page):

https://github.com/biocodellc/rppo/

• 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.):

This package fits under data retrieval since it is used in downloading/extracting data from the global plant phenology data portal.

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

The target audience are scientists researching plant phenology patterns, shifts of plant phenological patterns over time and space, climate change biologists, and biodiversity scientists looking for sources of plant observation data.

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

There are no other R packages that we know of that do the same thing.

•   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.

We enquired with @sckott and @karthik several weeks ago.

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:

[annakrystalli]

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

Hello @jdeck88, sorry for the slight delay and many thanks for your submission! An interesting package.

So there's a few issues flagged by the initial editol checks:

testthat.R missing

The package repository is missing a testthat.R script in the tests/ directory. Because of this, running covr::package_coverage() returns 0% coverage. Using usethis::use_testthat() creates the required file and the tests run as expected.

• Create testthat.R file.
• Add test coverage as part of CI and a badge for it in the README. (See ?usethis::use_coverage())

goodpractice::gp output

── GP rppo ──────────────────────────────────────────────────────────────────────────────────────
  It is good practice to
 
  ✖ write unit tests for all functions, and all package code in general. 75%
    of code lines are covered by test cases.

    R/ppo_data.R:74:NA
    R/ppo_data.R:75:NA
    R/ppo_data.R:76:NA
    R/ppo_data.R:77:NA
    R/ppo_data.R:78:NA
    ... and 23 more lines

• reviewers note highlighted coverage gaps that, inspect what is not covered to see if you think important areas are missed.

  ✖ omit "Date" in DESCRIPTION. It is not required and it gets invalid quite
    often. A build date will be added to the package when you perform `R CMD build` on
    it.
     

• omit "Date" in DESCRIPTION

  ✖ add a "URL" field to DESCRIPTION. It helps users find information about
    your package online. If your package does not have a homepage, add an URL to
    GitHub, or the CRAN package package page.

• add a "URL" field to DESCRIPTION

  ✖ add a "BugReports" field to DESCRIPTION, and point it to a bug tracker.
    Many online code hosting services provide bug trackers for free,
    https://github.com, https://gitlab.com, etc.

• add a "BugReports" field to DESCRIPTION

  ✖ use '<-' for assignment instead of '='. '<-' is the standard, and R
    users and developers are used it and it is easier to read your code for them if
    you use '<-'.

    R/ppo_data.R:37:19
    R/ppo_data.R:39:18
    R/ppo_data.R:54:11
    R/ppo_data.R:74:12
    R/ppo_data.R:75:12
    ... and 11 more lines

• Change '=' assignement 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/ppo_data.R:33:1
    R/ppo_data.R:39:1
    R/ppo_data.R:50:1
    R/ppo_data.R:58:1
    R/ppo_data.R:72:1
    ... and 5 more lines

• check code line length

  ✖ omit trailing semicolons from code lines. They are not needed and most R
    coding standards forbid them

    R/ppo_data.R:41:64
    R/ppo_data.R:119:32
    R/ppo_data.R:120:17
    R/ppo_terms.R:35:59

• omit trailing semicolons

  ✖ not import packages as a whole, as this can cause name clashes between
    the imported packages. Instead, import only the specific functions you need.

• reviewers to consider and give feedback on

  ✖ fix this R CMD check NOTE: Namespace in Imports field not imported from:
    ‘leafletR’ All declared Imports should be used.

• Needs checking. Usually this means you have a package (leafletR) in Imports that should really be in Suggests (perhaps it is only used in a vignette).

    
    
───────────────────────────────────────────────────────────────────────────────────────────────── 
> 

devtools::spell_check()

Flags some potential spelling errors of which only this looks genuine:

pouplates      ppo_terms.Rd:20

CC0 License.

Although the CC0 license specified in the DESCRIPTION is accepted by CRAN, it is not accepted by OSI. We recommend avoiding it unless you have a specific need to use it and suggest considering MIT as a similarly permissible license.

Happy to start looking for reviewers. I recommend using this time to try and address some of the issues raised so they can be checked during review rather that be reflagged.

Let me know if anything is unclear!

---

Reviewers:
Due date:

[jdeck88]

Thank you for the comments Anna..
I have addressed all of the issues that you brought up and committed my changes to our Github repo.

[annakrystalli]

Thanks for your prompt response @jdeck88! I've found the first reviewer and just trying to secure the second one. Will keep you posted. 👍

[annakrystalli]

Both reviewers have now been assigned! 🎉

---

Reviewers: @tdjames1 & @remsamp
Due date: 2018-05-04

[annakrystalli]

👋 @tdjames1 & @remsamp. Just checking in to make sure you're review is going ok? Feel free to reach out if have any questions 😊

[tdjames1]

@annakrystalli I'm just getting onto the review now, apologies for the delay. I'm aiming to get it done over this weekend.

[annakrystalli]

No problem @tdjames1, thanks for letting me know. I'll push back due date to the 7th then.

---

Reviewers: @tdjames1 & @remsamp
Updated due date: 2018-05-07