dwctaxon: Tools for Working with Darwin Core Taxon Data #574

joelnitta · 2023-02-16T07:49:48Z

Date accepted: 2023-05-22
Submitting Author Name: Joel H. Nitta
Submitting Author Github Handle: @joelnitta
Repository: https://github.com/joelnitta/dwctaxon
Version submitted: 1.0.0.9000
Submission type: Standard
Editor: @noamross
Reviewers: @collinschwantes, @sformel-usgs

Archive: TBD
Version accepted: TBD
Language: en

Paste the full DESCRIPTION file inside a code block below:

Package: dwctaxon
Title: Tools for Working with Darwin Core Taxon Data
Version: 1.0.0.9000
Authors@R: 
    c(
      person(given = "Joel H.",
           family = "Nitta",
           role = c("aut", "cre"),
           email = "joelnitta@gmail.com",
           comment = c(ORCID = "0000-0003-4719-7472")),
      person(given = "Wataru",
           family = "Iwasaki",
           role = c("ctb"),
           comment = c(ORCID = "0000-0002-9169-9245"))
    )
Description: Provides functions to create, manipulate, and validate taxonomic 
    data in compliance with Darwin Core standards 
    (Darwin Core "Taxon" class https://dwc.tdwg.org/terms/#taxon).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(
    markdown = TRUE,
    roclets = c("collate", "namespace", "rd", "roxyglobals::global_roclet"))
RoxygenNote: 7.2.1
Imports: 
    assertr,
    assertthat,
    digest,
    dplyr,
    glue,
    purrr,
    rlang,
    settings,
    stringr,
    tibble,
    utils
Suggests: 
    testthat (>= 3.0.0),
    roxyglobals (>= 0.2.1),
    mockery,
    readr,
    usethis,
    knitr,
    rmarkdown,
    tidyverse,
    patrick,
    stringi
Remotes: 
    anthonynorth/roxyglobals
Depends: 
    R (>= 2.10)
Config/testthat/edition: 3
URL: https://joelnitta.github.io/dwctaxon/,
    https://github.com/joelnitta/dwctaxon
BugReports: https://github.com/joelnitta/dwctaxon/issues
VignetteBuilder: knitr

Scope

Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):
- data retrieval
- data extraction
- data munging
- data deposition
- data validation and testing
- workflow automation
- version control
- citation management and bibliometrics
- scientific software wrappers
- field and lab reproducibility tools
- database software bindings
- geospatial data
- text analysis
Explain how and why the package falls under these categories (briefly, 1-2 sentences):

dwctaxon facilitates manipulating and validating taxonomic data (of biological species) in R, in compliance with the widely used Darwin Core data standard.

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

Biologists, anybody working with taxonomic data in Darwin Core format.

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

Not currently, to the best of my knowledge. The closest thing out there is the GBIF data validator (not an R package). The archived finch package had a function to call the GBIF data validator.

(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?

Not applicable

If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

No pre-submission inquiry

Explain reasons for any pkgcheck items which your package is unable to pass.

pkgcheck passes when I run it locally. I have observed an error in the CI, but I believe this is a problem with pkgcheck, and unrelated to my package.

Technical checks

Confirm each of the following by checking the box.

I have read the rOpenSci packaging guide.
I have read the author guide and I expect to maintain this package for at least 2 years or to find a replacement.

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, created with roxygen2.
contains a vignette with examples of its essential functions and uses.
has a test suite.
has continuous integration, including reporting of test coverage.

Publication options

Do you intend for this package to go on CRAN?
Do you intend for this package to go on Bioconductor?
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MEE Options

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Code of conduct

I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

The text was updated successfully, but these errors were encountered:

ropensci-review-bot · 2023-02-16T07:49:50Z

Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type @ropensci-review-bot help for help.

ropensci-review-bot · 2023-02-16T07:49:52Z

🚀

Editor check started

👋

ropensci-review-bot · 2023-02-16T10:52:29Z

Checks for dwctaxon (v1.0.0.9000)

git hash: db71df7b

✔️ Package name is available
✔️ has a 'codemeta.json' file.
✔️ has a 'contributing' file.
✔️ uses 'roxygen2'.
✔️ 'DESCRIPTION' has a URL field.
✔️ 'DESCRIPTION' has a BugReports field.
✔️ Package has at least one HTML vignette
✔️ All functions have examples.
✔️ Package has continuous integration checks.
✔️ Package coverage is 96.8%.
✔️ R CMD check found no errors.
✔️ R CMD check found no warnings.

Package License: MIT + file LICENSE

1. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.

type	package	ncalls
internal	base	83
internal	dwctaxon	28
internal	graphics	1
internal	stats	1
imports	glue	48
imports	settings	23
imports	dplyr	9
imports	stringr	6
imports	utils	5
imports	purrr	4
imports	tibble	2
imports	assertr	1
imports	assertthat	NA
imports	digest	NA
imports	rlang	NA
suggests	testthat	NA
suggests	roxyglobals	NA
suggests	mockery	NA
suggests	readr	NA
suggests	usethis	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	tidyverse	NA
suggests	patrick	NA
suggests	stringi	NA
linking_to	NA	NA

Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table.

base

list (12), is.na (9), paste (9), c (6), do.call (5), grepl (5), as.character (4), col (3), colnames (3), inherits (3), nrow (3), class (2), match (2), Sys.time (2), by (1), duplicated (1), for (1), formals (1), gsub (1), if (1), ifelse (1), is.null (1), isTRUE (1), lapply (1), seq_len (1), setdiff (1), strsplit (1), tryCatch (1), warning (1)

glue

glue (46), glue_collapse (1), identity_transformer (1)

dwctaxon

null_transformer (8), assert_that_d (2), any_not_true (1), assert_col (1), assert_dat (1), assert_that_uses_one_name (1), bind_rows_f (1), check_acc_id_has_tax_status (1), check_acc_id_valid_tax_status (1), check_accepted_map_to_nothing (1), check_col_names_p (1), check_fill_usage_id_name (1), check_mapping_exists (1), check_mapping_strict_status (1), check_mapping_to_self (1), check_sci_name_is_uniq (1), check_sci_name_not_na (1), dct_modify_row (1), dct_options (1), paste3 (1)

settings

inlist (22), options_manager (1)

dplyr

mutate (4), filter (3), anti_join (1), bind_rows (1)

stringr

fixed (4), str_detect (1), str_match (1)

utils

data (4), capture.output (1)

purrr

map_lgl (4)

tibble

tibble (2)

assertr

success_logical (1)

graphics

text (1)

stats

df (1)

NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.

2. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has:

code in R (100% in 17 files) and
1 authors
3 vignettes
2 internal data files
11 imported packages
9 exported functions (median 29 lines of code)
106 non-exported functions in R (median 11 lines of code)

Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
The following terminology is used:

loc = "Lines of Code"
fn = "function"
exp/not_exp = exported / not exported

All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the checks_to_markdown() function

The final measure (fn_call_network_size) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile.

measure	value	percentile	noteworthy
files_R	17	76.7
files_vignettes	3	92.4
files_tests	14	93.8
loc_R	2343	86.9
loc_vignettes	324	66.2
loc_tests	2584	95.6	TRUE
num_vignettes	3	94.2
data_size_total	28214	76.8
data_size_median	14107	81.1
n_fns_r	115	79.7
n_fns_r_exported	9	42.0
n_fns_r_not_exported	106	84.9
n_fns_per_file_r	5	67.9
num_params_per_fn	5	69.6
loc_per_fn_r	12	36.1
loc_per_fn_r_exp	29	61.6
loc_per_fn_r_not_exp	11	35.4
rel_whitespace_R	7	65.5
rel_whitespace_vignettes	43	75.5
rel_whitespace_tests	4	74.5
doclines_per_fn_exp	65	76.5
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	213	89.2

2a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

3. `goodpractice` and other checks

Details of goodpractice checks (click to open)

3a. Continuous Integration Badges

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
4191806772	pages build and deployment	success	9e0773	35	2023-02-16
4191789240	pkgcheck	NA	db71df	7	2023-02-16
4191789239	pkgdown	success	db71df	51	2023-02-16
4191789237	test-coverage	success	db71df	26	2023-02-16

3b. `goodpractice` results

`R CMD check` with rcmdcheck

R CMD check generated the following check_fail:

cyclocomp

Test coverage with covr

Package coverage: 96.81

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
dct_modify_row_single	103
dct_add_row	32
dct_opts	19
check_acc_id_has_tax_status	18
check_acc_id_valid_tax_status	18
check_accepted_map_to_nothing	18
check_syn_map_to_acc	18
check_variant_map_to_nonvar	18
check_variant_map_to_something	18
check_mapping_exists	17
check_mapping_to_self	17
dct_validate	17

Static code analyses with lintr

lintr found the following 10 potential issues:

message	number of times
Avoid library() and require() calls in packages	10

Package Versions

package	version
pkgstats	0.1.3
pkgcheck	0.1.1.11

Editor-in-Chief Instructions:

This package is in top shape and may be passed on to a handling editor

maurolepore · 2023-02-16T11:02:36Z

@joelnitta thanks a lot for your submision!
The checks are looking great. I'll check fit and overlap and come back to you asap.

maurolepore · 2023-02-28T10:20:43Z

@joelnitta thanks a lot for your patience.

I discussed with other editors and think this submission is in scope. I'll start looking for a handling editor.

joelnitta · 2023-02-28T10:56:36Z

Great, thanks @maurolepore!

maurolepore · 2023-02-28T12:25:24Z

@ropensci-review-bot assign @noamross as editor

ropensci-review-bot · 2023-02-28T12:25:27Z

Assigned! @noamross is now the editor

noamross · 2023-02-28T22:22:42Z

@ropensci-review-bot seeking reviewers

ropensci-review-bot · 2023-02-28T22:22:44Z

Please add this badge to the README of your package repository:

[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/574_status.svg)](https://github.com/ropensci/software-review/issues/574)

Furthermore, if your package does not have a NEWS.md file yet, please create one to capture the changes made during the review process. See https://devguide.ropensci.org/releasing.html#news

noamross · 2023-03-01T19:55:49Z

@ropensci-review-bot assign @collinschwantes as reviewer

ropensci-review-bot · 2023-03-01T19:55:52Z

@collinschwantes added to the reviewers list. Review due date is 2023-03-22. Thanks @collinschwantes for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

ropensci-review-bot · 2023-03-01T19:55:57Z

@collinschwantes: If you haven't done so, please fill this form for us to update our reviewers records.

noamross · 2023-03-01T19:59:18Z

Thanks @collinschwantes! Please be sure to look at the diagnostic report above. I note a few instances of packages imported for very few functions (assertr), high-cyclocomplexity functions that may benefit from breaking up, and some other goodpractice notes that should be examined as part of your review.

ropensci-review-bot · 2023-03-20T19:55:54Z

📆 @collinschwantes you have 2 days left before the due date for your review (2023-03-22).

noamross · 2023-04-25T13:28:46Z

@ropensci-review-bot submit review #574 (comment) time 8

ropensci-review-bot · 2023-04-25T13:28:50Z

Logged review for collinschwantes (hours: 8)

noamross · 2023-04-25T13:29:24Z

@ropensci-review-bot submit review #574 (comment) time 8

ropensci-review-bot · 2023-04-25T13:29:26Z

Logged review for sformel-usgs (hours: 8)

ropensci-review-bot · 2023-05-07T13:29:29Z

@joelnitta: please post your response with @ropensci-review-bot submit response <url to issue comment> if you haven't done so already (this is an automatic reminder).

Here's the author guide for response. https://devguide.ropensci.org/authors-guide.html

joelnitta · 2023-05-08T08:22:51Z

@ropensci-review-bot submit response ropensci/dwctaxon@82aa4ea

Thanks again to the reviewers for their helpful comments! Here are my responses.

Responses to @sformel-usgs

Review Comments

I found this package to be thoughtfully written and documented. Code appears to have been carefully constructed and functions well. However, I do have a few high level concerns:

TL;DR More context and example should be added to the statement of need.

The Statement of Need has been clarified in the README (ropensci/dwctaxon@c866731).

I’m not sure why these functions shouldn’t be included as part of the taxastand package (or vice versa)? Again, the video referenced above give some sense of why these tasks would be separated, but I think a little more description of how they relate could be useful. I’m not totally convinced that the modification/validation of taxonomic data (dwctaxon) should be separated from the standardization of species names from different sources (taxastand) as these tasks seem to have a lot of overlap.

Usage of dwctaxon is not limited to standardization of species names, as described in the revised Statement of Need and demonstrated in the newly added "Real World Data" vignette. Furthermore, different packages / software are available to do name standardization (e.g., U.Taxonstand in addition to taxastand). So in the case of name standardization, I think it makes more since to provide dwctaxon as a separate tool that can be used to prepare the reference database, then the user could standardize names against the reference using the tool of their choice.

Documentation

Throughout the documentation, but most noticeably in the vignette ‘What is DWC?’ vignette, Darwin Core is abbreviated ‘DWC’. Generally speaking, I see/use ‘DwC’, and that is what is described on the Wikipedia page since 2011. Not critical, but I would be curious to hear whether the author has a strong opinion on the appropriate abbreviation. If not, I would prefer DwC.

"DWC" has been changed to "DwC" throughout (ropensci/dwctaxon@fd1e149).

In the ‘What is DWC?’ vignette, line 64 describes genus, family and order as “higher taxonomic levels”. I understand these to be “lower levels”, which seems consistent with the comment in the DwC taxonomic term higherClassification.

The wording has been changed to "taxonomic levels above species" (ropensci/dwctaxon@0696416).

Line 64 of the editing vignette references ‘hash’ generically. I think it would be worth specifying that it is using MD5.

It is now specified that MD5 is used (ropensci/dwctaxon@ef7c393).

utils.R credits the paste3 function to a stackoverflow conversation. I’m not sure of the best way to give credit in this situation, but it seems like it would also be good to include the user [“IRTFM”] and userID [“1855677”], since it is a function that is clearly written by one person.

paste3() is no longer used (ropensci/dwctaxon@d25180c).

Logical programming API

Yes, however see suggestions below.

In the function, dct_add_row, I’m curious about the decision to only use the first 8 characters from the hash as the taxonID. As you note, this may result in duplicates, why not preserve the entire hash as taxonID?

Now the entire MD5 is used by default, and there is an option to use fewer characters (ropensci/dwctaxon@ef7c393).

I disagree with the use/creation of aliases as described in lines 72-89 of the editing vignette. This promotes confusion about the name of the DwC standard term. Especially in this case where the term is a function parameter and users can use tab to autocomplete, rather than typing out the names. I think this aspect of the package should be revised, and the vignette can point out tab autocomplete as a way to avoid typing out the rather long names of DwC.

These aliases are no longer used (ropensci/dwctaxon@b119623).

automated tool review

Checking the initial package report generated by our @ropensci-review-bot.

As noted in the goodpractice checks, dct_modify_row and dct_add_row have high-cyclocomplexity. I don’t have any great suggestions for ways to break it up. But, if my suggestion, that aliases for DwC terms should be avoided, is accepted, then some of the checks for misuse of aliases could be removed.

dct_modify_row_single() previously had the highest cyclocomplexity (103). Numerous subfunctions have been split out from dct_modify_row_single(), and there are no longer any if() statements in the main function, greatly decreasing cyclocomplexity to 14 (ropensci/dwctaxon@315bd19). Unfortunately one of the subfunctions, create_new_row_by_modification() still contains a large number of if() statements and has high cyclocomplexity (56), but this is a significant improvement from 103. I would like to avoid further breaking up create_new_row_by_modification() because it has a well-defined purpose (creating a single row), and it is easier to understand the conditional relationships when they are all at the same level and immediately visible.

The library and require calls described by lintr in goodpractices are acceptable. They all appear to be associated with vignettes, tests, or documentation of raw data creation.

It appears that the assertr package is imported for a single function in utilties.R. I don’t know of a simple way to replace this function and reduce the dependency.

Thanks for catching this. That function is no longer needed and has been removed, along with the dependency on assertr (ropensci/dwctaxon@b60ddd8).

Responses to @collinschwantes

Review Comments

Overall easy to use and well documented. I really enjoyed testing this package. That being said, the statement of need could more clearly define who the target audience is. Is it biologist who are not necessarily taxonomists, taxonomists, collections managers?

The target audience is anybody who needs to maintain DwC taxonomic data and uses R. The Statement of Need has been clarified and use-cases added (ropensci/dwctaxon@c866731).

I tested the package using data from a project I worked on back in 2014. Once I had the taxa data in the proper form, all functions worked as expected. I did notice that certain functions create missing columns or provide errors for non-dct terms. Its not always obvious which functions will generate new columns, and which wont. See dct_fill_col vs dct_add_row

Documentation has been added to clarify when new columns are added (ropensci/dwctaxon@9cb465e). Non-dct terms are never added as new columns.

I would prefer that functions use DCW terms instead of abbreviations.
I didn't find the terms saved me that much time from a typing perspective
and I had to remember the abbreviation plus the actual term. Not a lot of mental effort
but non-zero.

These aliases are no longer used (ropensci/dwctaxon@b119623).

Since there is an "add_row" function, it may be worth including a drop_row?

Thanks for the suggestion. This has been added as dct_drop_row() (ropensci/dwctaxon@54ba041).

dct_fill_col does not throw an error if the fill_from argument is a non-existent column that is a dct_term.

Thanks for pointing out this bug, it has been fixed (ropensci/dwctaxon@3f52a9c).

One error for failing test when running devtools::check. dct_add_row throws an error.

It is not clear to me what error this was, but in its current state devtools::check() passes locally and on CI builds.

dct_modify_row_single has a lot of if statements that are nicely labelled in the function. Consider whether or not each of those sections of the function could be split into its own, smaller, easier to evaluate function.

Thanks for the suggestion. Several sections of dct_modify_row_single() have been split into subfunctions (ropensci/dwctaxon@315bd19).

You could also take advantage of rlang::empty to test if something is NA or
NULL.

I have been able to clean up this code by moving the call to is.null() as one of the conditionals checked with assert_that() instead of running assert_that() conditional on the result of is.null() (ropensci/dwctaxon@712d07e).

The dependency section in the packaging guidelines recommends using minimum version numbers
for the package dependencies

The packaging guidelines only recommend using minimum version numbers if there is a known minimum version that would otherwise cause the package to break. I am not aware of any, so I did not include them.

Would be great (though potentially out of scope for the package) to have a
vignette that shows how to retrieve taxon data and/or what
you can do with taxon data once you have it properly formatted in Darwin core.

Thanks for the suggestion. This has been added as the "Real World Data" vignette (ropensci/dwctaxon@2af31e9)

sformel-usgs · 2023-05-09T13:33:47Z

Thanks @joelnitta , these are all satisfactory responses and revisions. I appreciate the changes you've made to the Statement of Need and the References in the readme. The Real World vignette was also a great addition for folks who might be starting out in this realm.

I rechecked the package and only came across one minor issue. On my Windows computer, the real-world data vignette fails to build because the download.file call results in a corrupt zip file. A solution is to add mode = "wb". But you should double check this, because I'm not 100% that it won't cause problems for non-Windows machines. This is something new that just started occurring for me (non-text files becoming corrupt). I'm not sure what changed, but apparently, it's not unusual.

sformel-usgs · 2023-05-10T14:49:13Z

Thanks for handling that so quickly! Everything is working smoothly now. I have no more suggestions or concerns.

noamross · 2023-05-10T14:52:31Z

Thank your for the robust reply @joelnitta and your follow-up, @sformel-usgs. @collinschwantes, please look at the changes to the package and indicate if they address your review.

collinschwantes · 2023-05-19T16:45:40Z

@joelnitta Looks great!! The real world example is very helpful! No more suggestions or concerns.

noamross · 2023-05-22T15:17:12Z

@ropensci-review-bot approve dwctaxon

ropensci-review-bot · 2023-05-22T15:17:14Z

Approved! Thanks @joelnitta for submitting and @collinschwantes, @sformel-usgs for your reviews! 😁

To-dos:

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).

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We maintain an online book with our best practice and tips, this chapter starts the 3d section that's about guidance for after onboarding (with advice on releases, package marketing, GitHub grooming); the guide also feature CRAN gotchas. Please tell us what could be improved.

Last but not least, you can volunteer as a reviewer via filling a short form.

joelnitta · 2023-05-24T03:16:22Z

@ropensci-review-bot finalize transfer of dwctaxon

ropensci-review-bot · 2023-05-24T03:16:25Z

Transfer completed.
The dwctaxon team is now owner of the repository and the author has been invited to the team

joelnitta · 2023-05-25T05:35:54Z

Thanks again to reviewers @sformel-usgs and @collinschwantes and editor @noamross !

I have completed all of the tasks above:

I'm happy this package now has a home at rOpenSci!

This was referenced Feb 16, 2023

Check for non-used imports ropensci/dwctaxon#43

Closed

New function to exchange data using the Darwing Core Standard ropensci/taxlist#37

Closed

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ropensci-review-bot added 1/editor-checks and removed 0/editorial-team-prep labels Feb 28, 2023

ropensci-review-bot added 2/seeking-reviewer(s) and removed 1/editor-checks labels Feb 28, 2023

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joelnitta mentioned this issue Apr 25, 2023

Should add vignette showing how to fetch data ropensci/dwctaxon#53

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ropensci-review-bot added 4/review(s)-in-awaiting-changes and removed 3/reviewer(s)-assigned labels Apr 25, 2023

This was referenced May 8, 2023

assertr is causing a dependency but only gets used in one function ropensci/dwctaxon#66

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Not clear when new columns are added ropensci/dwctaxon#68

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Feature request: function to drop a row ropensci/dwctaxon#70

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joelnitta mentioned this issue May 9, 2023

Real-world data vignette fails on some Windows computers ropensci/dwctaxon#73

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noamross added 5/awaiting-reviewer(s)-response and removed 4/review(s)-in-awaiting-changes labels May 10, 2023

ropensci-review-bot added 6/approved and removed 5/awaiting-reviewer(s)-response labels May 22, 2023

ropensci-review-bot closed this as completed May 22, 2023

joelnitta mentioned this issue May 25, 2023

Reviewers missing from author list ropensci/dwctaxon#81

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joelnitta mentioned this issue Dec 19, 2023

[PRE REVIEW]: dwctaxon, an R package for editing and validating taxonomic data in Darwin Core format openjournals/joss-reviews#6163

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Kevin-Mattheus-Moerman mentioned this issue Jan 11, 2024

[REVIEW]: dwctaxon, an R package for editing and validating taxonomic data in Darwin Core format openjournals/joss-reviews#6215

Closed

dwctaxon: Tools for Working with Darwin Core Taxon Data #574

dwctaxon: Tools for Working with Darwin Core Taxon Data #574

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joelnitta commented Feb 16, 2023 • edited by ropensci-review-bot Loading

Archive: TBD Version accepted: TBD Language: en

Scope

Technical checks

Publication options

Code of conduct

ropensci-review-bot commented Feb 16, 2023

ropensci-review-bot commented Feb 16, 2023

ropensci-review-bot commented Feb 16, 2023

Checks for dwctaxon (v1.0.0.9000)

1. Package Dependencies

2. Statistical Properties

2a. Network visualisation

3. goodpractice and other checks

3a. Continuous Integration Badges

3b. goodpractice results

R CMD check with rcmdcheck

Test coverage with covr

Cyclocomplexity with cyclocomp

Static code analyses with lintr

Editor-in-Chief Instructions:

maurolepore commented Feb 16, 2023

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joelnitta commented Feb 28, 2023

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noamross commented Apr 25, 2023

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joelnitta commented May 8, 2023

Responses to @sformel-usgs

Review Comments

Documentation

Logical programming API

automated tool review

Responses to @collinschwantes

Review Comments

sformel-usgs commented May 9, 2023

sformel-usgs commented May 10, 2023

noamross commented May 10, 2023

collinschwantes commented May 19, 2023

noamross commented May 22, 2023

ropensci-review-bot commented May 22, 2023

joelnitta commented May 24, 2023

ropensci-review-bot commented May 24, 2023

joelnitta commented May 25, 2023

joelnitta commented Feb 16, 2023 •

edited by ropensci-review-bot

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Archive: TBD
Version accepted: TBD
Language: en

3. `goodpractice` and other checks

3b. `goodpractice` results

`R CMD check` with rcmdcheck