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:

• 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:

@arendsee
@zachary-foster
@sckott

[maelle]

Thanks for your submission @kamapu, we're discussing and will get back to you soon.

[maelle]

👋 again @kamapu, it's a bit of a tricky situation and we're going to need more information about your package before making a decision.

The general question is: how would an R user with a taxonomy problem at hand know how to choose one of the two packages?

Your answer could be a table as in this pre-submission inquiry or a decision tree. I know it's a bit of work that might not even warrant onboarding, but it'd be something useful to have in the docs of your package (and of taxa probably) since the existence of both packages even not under the rOpenSci's umbrella mean users might have to make a decision.

Thanks for your patience!

[maelle]

👋 @kamapu! Any update or answer on the above? Thank you!

[maelle]

👋 @kamapu! Any update or answer on the above? Thank you!

[kamapu]

Dear @maelle, there are not really updates on this issue. At the moment I am for a longer period in the field (Kenya). Though, it will be difficult for me to really document differences between taxlist and taxa. I only can tell in favour of taxlist that this package is implemented in vegtable, which is meant as a container for vegetation-plot databases in R. In fact, taxlist development runs in parallel to vegtable but they are kept in separated packages due to the complexity of taxonomic structures and the potential integration of taxonomic lists in other object classes.

Now my question is: Can I submit two packages as a bulk in ROpenSci or should I leave taxlist and try to submit vegtable alone?

Best regards!

[maelle]

One (pre-)submission by package is best.

Have a productive time in the field!

[kamapu]

Dear @maelle:

I went through most of the functions in the manual of taxa to have a better impression about differences between this package and taxlist. I have to recognize, it has been hard for me to understand the way how taxa deals with taxonomic information, since its programming style is a higher level than my primitive skills. Thus, the following comments should be interpreted as impressions rather than truth.

Basically both mentioned packages fulfil similar tasks but use different approaches, taxa uses a function-oriented approach (R6), while taxlist uses a data-oriented one (S4). Both packages attempt to provide an object class containing taxonomic information, but taxlist is strongly focusing on potential applications in vegetation-plot databases. taxlist allows diverse degrees of completeness, starting from just listing of taxonomic entities up to data sets including taxonomic ranks, synonyms, ecological traits (or further taxon attributes), and taxon views.

Contributions of taxlist

Further aspects are probably not implemented in taxa and can be considered as the contribution of taxlist to ROpenSci:

• While taxa is importing information from several on-line databases, taxlist offers alternatives of import data from local data sets. For instance data loaded in data frames can be converted by using the function df2taxlist(). There is also a function called tv2taxlist() for importing species lists included in Turboveg
• The consistency of information included in taxonomic lists is "cross-checked" by validity in S4 objects. In the case of taxlist, potential issues such as duplicated combinations, parent-child relationships that are not consistent to taxonomic ranks, etc. will generate error messages when creating new objects. It is not clear for me how those issues are handled in taxa
• I don't see any mentions to synonymy in taxa, which is a crucial feature in taxlist, assuming that all databases including data from different sources have to implement a way of linking taxon usage names (either accepted names or synonyms) with taxon concepts. There is no mention to taxon views in taxa, either
• A function backup_object() for inserting time stamps to backups produced by save()
• Some string process and comparisons through the functions dissect_name() (split names into single terms) and match_names() for comparing character values with names included in taxlist objects
• Interaction with knitr and rmarkdown for inserting taxon names in respective documents using the function print_name()

Features in Development

Additional features in development, which may not be yet included in taxa are:

• An object class for multiple taxon views (taxlist enable single taxon views per taxon concept)
• A plotting function displaying relations between taxon as dendrograms
• A function exporting the content of taxlist objects into the Veg-X standard

Final Remarks

I hope the previous comments properly support taxlist as a package rather complementary to taxa than redundant and make it eligible for ROpenSci. Disregarding the final decision, a way to make data sets exchangeable among those two applications should be strongly recommended.

[zachary-foster]

Thanks for looking through the docs/code @kamapu! Here are some thoughts:

While taxa is importing information from several on-line databases, taxlist offers alternatives of import data from local data sets.

taxa can read local datasets using parse_tax_data, but it does not have any parsers for specific local formats, since we wanted to keep everything generic.

The consistency of information included in taxonomic lists is "cross-checked" by validity in S4 objects.

Yep, taxa uses R6 classes which are not strong typed, so users can break the objects if they set fields manually instead of using our dplyr-like manipulation functions.

I don't see any mentions to synonymy in taxa, which is a crucial feature in taxlist

There is no such feature explicitly and we dont have plans for one at the moment

A plotting function displaying relations between taxon as dendrograms

taxa uses print_tree for this

A function exporting the content of taxlist objects into the Veg-X standard

I have no plans to support import or export of specific file formats in taxa, since it is primarily a data manipulation standard.

[sckott]

thanks @kamapu for the reply - we're discussing now