taxlist, a package for structuring taxonomic lists and related information

[kamapu]

Summary

• What does this package do? (explain in 50 words or less):

The taxlist package structures taxonomic information into S4 objects and implements methods for the manipulation of contained information. Such objects may or may not contain information on synonymy, taxonomic ranks, parent-child relations, taxon views (references used to establish relation between taxon usage names and taxon concepts), and taxon (functional) traits.

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

Package: taxlist
Version: 0.1.5
Encoding: UTF-8
Date: 2018-06-18
Title: Handling Taxonomic Lists
Authors@R:
    person("Miguel", "Alvarez", email="kamapu78@gmail.com", role=c("aut", "cre"))
Depends:
    R(>= 3.0.0),
    stats,
    utils
Imports:
    foreign,
    grDevices,
    methods,
    taxize,
    stringdist,
    vegdata
Suggests:
    ape,
    devtools,
    knitr,
    stringi,
    taxa,
    rmarkdown
LazyData: true
Description: Handling taxonomic lists through objects of class 'taxlist'.
    This package provides functions to import species lists from 'Turboveg'
    (<https://www.synbiosys.alterra.nl/turboveg>) and the possibility to create
    backups from resulting R-objects.
    Also quick displays are implemented as summary-methods.
License: GPL (>= 2)
URL:
    https://cran.r-project.org/package=taxlist,
    https://github.com/kamapu/taxlist
BugReports: https://github.com/kamapu/taxlist/issues
Collate:
    'NULLing.R''auxiliary_functions.R''deprecated-functions.R''dissect_name.R'
    'taxlist-class.R''clean.R''as.list.R''taxon_views.R''add_view.R'
    'taxon_names.R''taxon_relations.R''taxon_traits.R'
    'levels.R''add_concept.R''update_concept.R''add_synonym.R'
    'accepted_name.R''synonyms.R''basionym.R''update_name.R''delete_name.R'
    'replace_view.R''get_children.R'
    'change_concept.R''Extract.R''subset.R'
    'merge_taxa.R''backup_object.R''load_last.R''summary.R'
    'df2taxlist.R''tv2taxlist.R''tnrs.R''tax2traits.R''match_names.R''print_name.R'
    'StartMessage.R'
VignetteBuilder: knitr

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

https://github.com/kamapu/taxlist

• 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.):

Reproducibility, because this package makes taxonomic information available in a quasi-standard format and tests inconsistencies on the content of taxonomic lists.

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

In general to taxonomists and biodiversity scientists, in particular to vegetation ecologists (taxlist objects are implemented in the package vegtable).

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

While its functionality may overlap the package taxa, the package taxlist attempts to be flexible in the degree of completeness of data (incompleteness is very frequent in vegetation-plot databases), it is meant to be integrated in objects containing diversity information (as in the mentioned package vegtable) and to import data from local storage (spreadsheets, Turboveg data sets and even PostgreSQL tables by using vegtable2).

•   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:

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

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

• [x] 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:

@arendsee @zachary-foster @sckott

[mcsiple]

Yes, it looks good to me. Thank you @kamapu , @levisc8 and @maelle (and congratulations from me too!)

On Thu, Sep 17, 2020 at 12:02 AM Maëlle Salmon notifications@github.com wrote:

Thanks @kamapu https://github.com/kamapu and congrats again on the new family member!

@mcsiple https://github.com/mcsiple @levisc8 https://github.com/levisc8 are you ok with the response?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ropensci/software-review/issues/233#issuecomment-694003511, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAWM42UJRC6SOVICVT7MHM3SGGYB7ANCNFSM4FHQR3VQ .

--

---

Margaret (Megsie) Siple James S. McDonnell Postdoctoral Fellow Department of Ecology Evolution & Marine Biology University of California Santa Barbara

mobile: +1 (206) 661-8403

[levisc8]

Hi @kamapu @mcsiple @maelle , Sorry for the slow response - the changes look good to me as well. Congratulations on the newest addition to your family @kamapu!

[maelle]

Approved! Thanks @kamapu for submitting and @mcsiple @levisc8 for your reviews! :smile_cat:

To-dos:

• [ ] Transfer the repo to rOpenSci's "ropensci" GitHub organization under "Settings" in your repo. I have invited you to a team that should allow you to do so. You'll be made admin once you do.
• [ ] Fix all links to the GitHub repo to point to the repo under the ropensci organization.
• [ ] If you already had a pkgdown website and are ok relying only on rOpenSci central docs building and branding,
  • deactivate the automatic deployment you might have set up
  • remove styling tweaks from your pkgdown config but keep that config file
  • replace the whole current pkgdown website with a redirecting page
  • replace your package docs URL with https://docs.ropensci.org/package_name
  • In addition, in your DESCRIPTION file, include the docs link in the URL field alongside the link to the GitHub repository, e.g.: URL: https://docs.ropensci.org/foobar (website) https://github.com/ropensci/foobar
• [ ] Fix any links in badges for CI and coverage to point to the ropensci URL. We no longer transfer Appveyor projects to ropensci Appveyor account so after transfer of your repo to rOpenSci's "ropensci" GitHub organization the badge should be [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/ropensci/pkgname?branch=master&svg=true)](https://ci.appveyor.com/project/individualaccount/pkgname).
• [ ] We're starting to roll out software metadata files to all ropensci packages via the Codemeta initiative, see https://github.com/ropensci/codemetar/#codemetar for how to include it in your package, after installing the package - should be easy as running codemetar::write_codemeta() in the root of your package.

Should you want to acknowledge your reviewers in your package DESCRIPTION, you can do so by making them "rev"-type contributors in the Authors@R field (with their consent). More info on this here.

Welcome aboard! We'd love to host a post about your package - either a short introduction to it with an example for a technical audience or a longer post with some narrative about its development or something you learned, and an example of its use for a broader readership. If you are interested, consult the blog guide, and tag @stefaniebutland in your reply. She will get in touch about timing and can answer any questions.

We've put together an online book with our best practice and tips, this chapter starts the 3d section that's about guidance for after onboarding. Please tell us what could be improved, the corresponding repo is here.

[kamapu]

:partying_face: :partying_face: :partying_face: Then, there is some work to do, still. Surely I'll come back with some questions. Thanks to all participants in the development and review!

[maelle]

Please ping me once you've transferred the repo so that I might give you admin rights back, and feel free to ask me any question. Note that the invitation to the ropensci GitHub organization expires after I think one week. If you try to transfer the repo too late, tell me to re-send an invite.

[kamapu]

Transfer to ropensci

• [x] Transfer to ropensci repository
• [x] Fixed links Done in https://github.com/ropensci/taxlist/commit/d962046b6f80a7cf28a2956203ed178ffc146886
• [x] Redirect site to 'docs/ropensci' Done in https://github.com/ropensci/taxlist/commit/fab0ca5318f142c0ac60f611f388facb355136d6
• [x] Set links in badges Done by solving the second comment
• [x] Add codemeta.json Done in https://github.com/ropensci/taxlist/commit/89708aaffb7bc3ea4924741ff4c04b80e28b0bc5

[kamapu]

@maelle I just transferred the repository to ROpenSci and tried to respond to all bullet points accordingly. There is just one issue regarding to the new package site and the images. How can I include the figures to be displayed in docs/ropensci?

[maelle]

@kamapu I gave you admin rights again. I am not sure I follow your question. Where are those images now? What docs/ropensci deploys is a pkgdown website. I see images in https://docs.ropensci.org/taxlist/, what is missing?

[kamapu]

@maelle In the source of the package there is a folder README-figures, which contains a PNG-image of the taxlist data schema (Figure before chapter Installing taxlist) but is also used to store figures generated by plotting functions (barplot at the very bottom, before Acknowledgements). While these figures are visible in https://github.com/ropensci/taxlist/, they are missing in https://docs.ropensci.org/taxlist/

[maelle]

Does https://pkgdown.r-lib.org/reference/build_home.html#images-and-figures help?

[kamapu]

Oh, yes! @maelle I used the opportunity to add some improvements:

• Function match_names() is sorting results by similarity
• I included within the package code (folder inst) all data required by the vignette.

[maelle]

Awesome! Let me plug two blog posts of mine :grin:

• https://blog.r-hub.io/2020/06/03/vignettes/
• https://blog.r-hub.io/2020/05/29/distribute-data/

In any case I think I can close this issue but feel free to ask questions here / in the forum / etc.

Thanks all again!

[kamapu]

Thanks to everyone, also from my side. @maelle interesting posts. It seems to be, that my original idea of allocating data in a data package is not that bad at all... I wonder if this may be also a good practice for their use in examples within CRAN packages, assuming that the data-package may not be a CRAN-package...