Title:	Taxonomic Name Resolution Service
Version:	0.3.6
Description:	Provides access to the Taxonomic Name Resolution Service https://github.com/ojalaquellueva/tnrsapi through R. The user supplies plant taxonomic names and the package returns resolved taxonomic names along with information on decisions. Optionally, the package can also be used to parse taxonomic names.
License:	MIT + file LICENSE
Encoding:	UTF-8
LazyData:	true
Imports:	jsonlite, httr
Suggests:	knitr, rmarkdown, testthat, vcr (≥ 0.6.0), devtools
VignetteBuilder:	knitr
RoxygenNote:	7.2.3
Depends:	R (≥ 3.5.0)
NeedsCompilation:	no
Packaged:	2024-05-13 00:15:00 UTC; Brian Maitner
Author:	Brian Maitner [aut, cre], Brad Boyle [aut], Paul Efren [ctb]
Maintainer:	Brian Maitner <bmaitner@gmail.com>
Repository:	CRAN
Date/Publication:	2024-05-13 02:13:15 UTC

Resolve plant taxonomic names

Description

Resolve plant taxonomic names.

Usage

TNRS(
  taxonomic_names,
  sources = c("wcvp", "wfo"),
  classification = "wfo",
  mode = "resolve",
  matches = "best",
  accuracy = NULL,
  skip_internet_check = FALSE,
  ...
)

Arguments

Value

Dataframe containing TNRS results.

Note

wfo = World Flora Online, wcvp = World Checklist of Vascular Plants, cact = Cactaceae at Caryophyllales.org.

For queries of more than 5000 names, the function will automatically divide the query into batches of 5000 names and then run the batches one after the other. Thus, for very large queries this may take some time. When this is the case, a progress bar will be displayed.

IMPORTANT: Note that parallelization of queries is automatically handled by the API, and so there is no need to further parallelize in R (in fact, doing so may actually slow things down!).

Examples

## Not run: 
# Take a subset of the testfile to speed up runtime
tnrs_testfile <- tnrs_testfile[1:20, ]

results <- TNRS(taxonomic_names = tnrs_testfile)

# Inspect the results
head(results, 10)

## End(Not run)

Resolve a small batch of plant taxonomic names

Description

Resolve a small batch of plant taxonomic names

Usage

TNRS_base(
  taxonomic_names,
  sources = c("wcvp", "wfo"),
  classification = "wfo",
  mode = "resolve",
  matches = "best",
  accuracy = NULL,
  skip_internet_check = FALSE,
  ...
)

Arguments

Value

Dataframe containing TNRS results.

Note

This function is primarily used as an internal function of TNRS and can only handle relatively small batches of names.

usda = United States Department of Agriculture, wfo = World Flora Online, wcvp = World Checklist of Vascular Plants.

Get citation information

Description

Returns information needed to cite the TNRS

Usage

TNRS_citations(skip_internet_check = FALSE, ...)

Arguments

Value

Dataframe containing bibtex-formatted citation information

Note

This function provides citation information in bibtex format that can be used with reference manager software (e.g. Paperpile, Zotero). Please do remember to cite both the sources and the TNRS, as the TNRS couldn't exist without these sources!

Examples

{
  citation_info <- TNRS_citations()
}

Handle API access and format

Description

Internal function for handling accessing the API,data formatting, and errors

Usage

TNRS_core(
  url = "https://tnrsapi.xyz/tnrs_api.php",
  mode = "resolve",
  data_json = NULL,
  sources = c("wcvp", "wfo"),
  classification = "wfo",
  matches = "best",
  accuracy = NULL,
  batches = NULL
)

Arguments

Note

For more information on current sources, use the function TNRS_sources()

Get TNRS metadata

Description

Returns metadata on TNRS including version and citation information

Usage

TNRS_metadata(bibtex_file = NULL, skip_internet_check = FALSE)

Arguments

Value

List containing: (1) bibtex-formatted citation information, (2) information about TNRS data sources, and (3) TNRS version information.

Note

This function provides citation information in bibtex format that can be used with reference manager software (e.g. Paperpile, Zotero). Please remember to cite both the sources and the TNRS, as the TNRS couldn't exist without these sources!

This function is a wrapper that returns the output of the functions TNRS_citations, TNRS_sources, and TNRS_version.

Examples

{
  metadata <- TNRS_metadata()
}

Get information on sources used by the TNRS

Description

Return metadata about the current TNRS sources

Usage

TNRS_sources(skip_internet_check = FALSE, ...)

Arguments

Value

Dataframe containing information about the sources used in the current TNRS version.

Examples

{
  sources <- TNRS_sources()
}

Get synonyms for a single species

Description

Get synonyms for a single species

Usage

TNRS_synonyms(
  taxonomic_name,
  source = "wcvp",
  skip_internet_check = FALSE,
  ...
)

Arguments

Value

Dataframe containing synonyms and associated data for a single species.

Note

This function only handles a single source and a single taxonomic name at a time. This is by design.

wfo = World Flora Online, wcvp = World Checklist of Vascular Plants, cact = Cactaceae at Caryophyllales.org

Examples

{

TNRS_synonyms(taxonomic_name = "Sabal palmetto",source =  "wfo")

}

Get metadata on current TNRS version

Description

Return metadata about the current TNRS version

Usage

TNRS_version(skip_internet_check = FALSE, ...)

Arguments

Value

Dataframe containing current TNRS version number, build date, and code version.

Examples

{
  TNRS_version_metadata <- TNRS_version()
}

Check whether the internet is on

Description

Check for internet

Usage

check_internet()

Value

TRUE if internet connection is detected, FALSE otherwise.

100 scientific names.

Description

A dataset containing scientific names for 100 taxa. Names vary in accuracy and correctness.

Usage

tnrs_testfile

Format

A data frame with 100 rows and 2 variables:

ID

Unique integer identifying each row

taxon

Scientific name, possibly containing errors

...

Source

https://github.com/ojalaquellueva/TNRSapi