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="[email protected]", 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:

• 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/.
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  • (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:

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• 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