This package attempts to simplify the citation and formatting of taxonomic names in Markdown documents (R Markdown and Quarto) as well as in LaTeX (knitr).
To use this package, you need to have a taxonomic list imported into the taxlist package, including taxonomic ranks and parent-child relationships.
Assuming you are already working in one of the frameworks, either R
Mardown or Quarto, you will need to install taxnames on your own
system.
install.packages("taxnames", dependencies = TRUE)Alternatively, you can download the latest development version from GitHub using the package remotes.
library(remotes)
install_github("kamapu/taxnames")Before you continue, you will need to load the packages taxlist and
taxnames in your session.
library(taxlist)
library(taxnames)The package taxnames uses a taxonomic object formatted by taxlist
and stored in the background. If you manage to import your taxonomic
list to taxlist, you can then set your own standard taxonomy.
set_tax(your_taxlist_object)Per default taxnames takes the taxonomic list Easplist form the
package taxlist.
get_tax()
#> object size: 761.4 Kb
#> validation of 'taxlist' object: TRUE
#>
#> number of taxon usage names: 5393
#> number of taxon concepts: 3887
#> trait entries: 311
#> number of trait variables: 1
#> taxon views: 3
#>
#> concepts with parents: 3698
#> concepts with children: 1343
#>
#> hierarchical levels: form < variety < subspecies < species < complex < genus < family
#> number of concepts in level form: 2
#> number of concepts in level variety: 95
#> number of concepts in level subspecies: 71
#> number of concepts in level species: 2521
#> number of concepts in level complex: 1
#> number of concepts in level genus: 1011
#> number of concepts in level family: 186The main task of taxnames is to allow the formatting of taxonomic
names by linking documents to pre-formatted taxonomic lists. This avoids
typing errors (even experts make them) and allows reproducibility and
automation, especially for reporting on biodiversity.
We will select a target taxon using the keyword "papyrus".
# Match 'papyrus' with the taxonomic list
summary(get_tax(), "papyrus")
#> ------------------------------
#> concept ID: 206
#> view ID: 1
#> level: species
#> parent: 54853 Cyperus L.
#>
#> # accepted name:
#> 206 Cyperus papyrus L.
#>
#> # synonyms (2):
#> 52612 Cyperus papyrus ssp. antiquorum (Willd.) Chiov.
#> 52613 Cyperus papyrus ssp. nyassicus Chiov.
#> ------------------------------We pick the correspondent taxon identifier 206. Now we can use this ID to mention the taxon.
`r tn_fna(206)`, also known as papyrus, is a tall sedge
growing in reed-like swamp vegetation in shallow water.
`r tn_an(206)` has a very long history of use by humans as
one of the first types of paper ever made.
This will be rendered as
Cyperus papyrus L., also known as papyrus, is a tall sedge growing in reed-like swamp vegetation in shallow water. C. papyrus has a very long history of use by humans as one of the first types of paper ever made.
Functions provided by taxnames represent several formats for taxonomic
names.
| Description | Call | Output |
|---|---|---|
| Full name without author name | tn_fn(206) |
Cyperus papyrus |
| Full name with author name | tn_fna(206) |
Cyperus papyrus L. |
| Full name with author name and taxon view (secundum) | tn_fnas(206) |
Cyperus papyrus L. sec. African Plant Database (2012) |
| Abbreviated name without author name | tn_an(206) |
C. papyrus |
| Abbreviated name with author name | tn_ana(206) |
C. papyrus L. |
Analogous to them, there are functions defined for synonyms that format names by their name ID (TaxonUsageID) rather than by their taxon ID (TaxonConceptID). For example
The synonymous of `r tn_fna(206)` are
`r tn_funa(c(52612, 52613))`
Which is rendered as.
The synonymous of Cyperus papyrus L. are Cyperus papyrus ssp. antiquorum (Willd.) Chiov. and Cyperus papyrus ssp. nyassicus Chiov.
| Description | Call | Output |
|---|---|---|
| Full usage name without author name | tn_fun(52612) |
Cyperus papyrus ssp. antiquorum |
| Full usage name with author name | tn_funa(52612) |
Cyperus papyrus ssp. antiquorum (Willd.) Chiov. |
| Abbreviated usage name without author name | tn_aun(52612) |
C. papyrus ssp. antiquorum |
| Abbreviated usage name with author name | tn_auna(52612) |
C. papyrus ssp. antiquorum (Willd.) Chiov. |
Last but not least, it is possible to query parental taxa with additional functions (see the package manual). As a cross-check, we can first look at the indented list.
indented_list(get_tax(), "papyrus")
#> Cyperaceae Juss.
#> Cyperus L.
#> Cyperus papyrus L.The hierarchical classification can then be expressed in text as follows
`r tn_fna(206)` belongs to the genus `r tn_pfna(206, "genus")` and
to the family `r tn_pfna(206, "family", italics = FALSE)`
Cyperus papyrus L. belongs to the genus Cyperus L. and to the family Cyperaceae Juss.