Version:	0.1.0
Encoding:	UTF-8
Title:	Formatting Taxonomic Names in Markdown
Depends:	R (≥ 4.3.0)
Imports:	taxlist (≥ 0.3.0)
Suggests:	testthat (≥ 3.0.0)
Description:	A collection of functions used to format taxonomic names in Markdown documents. Those functions work with data structured according to Alvarez and Luebert (2018) <doi:10.3897/bdj.6.e23635>.
License:	GPL-3
URL:	https://github.com/kamapu/taxnames
BugReports:	https://github.com/kamapu/taxnames/issues
RoxygenNote:	7.3.1
NeedsCompilation:	no
Packaged:	2024-07-05 11:19:11 UTC; miguel
Author:	Miguel Alvarez [aut, cre]
Maintainer:	Miguel Alvarez <kamapu78@gmail.com>
Repository:	CRAN
Date/Publication:	2024-07-08 05:10:05 UTC

Get or set a global taxonomy

Description

For convenience and to simplify the call of name formats, the containing object (a taxlist::taxlist object) will be handled internally by all functions.

A standard taxonomic list is already set in this package and can be retrieved or replaced.

The function set_style() sets the style for the formatted names (default "markdown") and the standard collapse connectors.

Usage

set_tax(tax)

## S3 method for class 'taxlist'
set_tax(tax)

get_tax()

set_style(style, collapse, secundum)

get_style()

Arguments

Value

get_tax() returns an object of class taxlist::taxlist, while get_style() returns a list with options set for the session.

Examples

## Get the current taxonomy
get_tax()

## Get further settings
get_style()

Standard formats for accepted names

Description

Inserting formatted taxonomic names in documents require specific functions for every format, which are provided here.

These functions print only accepted names for the selected taxon concepts.

Suffixes in the function names are explained as follows:

• fn: Full name without author name.

• fna: Full name with author name.

• fnas: Full name with author name and taxon view (secundum).

• an: Abbreviated name without author name.

• ana: Abbreviated name with author name.

Usage

tn_fn(x, ...)

tn_fna(x, ...)

tn_fnas(x, ...)

tn_an(x, ...)

tn_ana(x, ...)

Arguments

Value

All these functions return a character value.

Examples

## Compare all these outputs
tn_fn(13)
tn_fna(13)
tn_fnas(13)
tn_an(13)
tn_ana(13)

Standard formats for taxonomic names

Description

These functions work similarly to tn_an() and its alies but the names are accessed by their TaxonUsageID and work also for synonyms.

Suffixes in the function names are explained as follows:

• fun: Full usage name without author name.

• funa: Full usage name with author name.

• aun: Abbreviated usage name without author name.

• auna: Abbreviated usage name with author name.

Usage

tn_fun(x, ...)

tn_funa(x, ...)

tn_aun(x, ...)

tn_auna(x, ...)

Arguments

Value

All these functions return a character value.

Examples

## Compare all these outputs
tn_fun(52613)
tn_funa(52613)
tn_aun(52613)
tn_auna(52613)

Print formatted names for parents

Description

Displaying names of parent taxa.

Suffixes in the function names are explained as follows:

• pfn: Parent's full name without author name.

• pfna: Parent's full name with author name.

• pfnas: Parent's full name with author name and taxon view (secundum).

• pan: Parent's abbreviated name without author name.

• pana: Parent's abbreviated name with author name.

Usage

tn_pfn(x, level, ...)

tn_pfna(x, level, ...)

tn_pfnas(x, level, ...)

tn_pan(x, level, ...)

tn_pana(x, level, ...)

Arguments

Value

All these functions return a character value.

Examples

## Compare all these outputs
tn_pfn(13, "family")
tn_pfna(13, "family")
tn_pfnas(13, "family")
tn_pan(13, "family")
tn_pana(13, "family")