Format usage names for publications

When writing on bio-diversity, usage names could be automatically inserted in documents including the typical italic format for different elements of a scientific name. The function print_name can be applied either in markdown documents or for graphics.

In Rmarkdown documents use *Cyperus papyrus* L. for inserting a formatted a species name.

Usage

print_name(object, ...)

# S3 method for class 'character'
print_name(
  object,
  second_mention = FALSE,
  style = "markdown",
  isolate = c("var.", "ssp.", "subsp.", "f.", "fma."),
  trim = c("spp.", "sp.", "species"),
  italics = TRUE,
  collapse,
  ...
)

# S3 method for class 'taxlist'
print_name(
  object,
  id,
  concept = TRUE,
  include_author = TRUE,
  secundum,
  style = "markdown",
  italics = TRUE,
  collapse,
  ...
)

Arguments

object

An object of class taxlist.

...

Further arguments passed among methods.

second_mention

Logical value, whether the genus name should be abbreviated or not.

style

Character value indicating the alternative format for italics. The available options are "markdown" (called within Rmarkdown documents), "html" (for documents rendered into html files), "expression" (used for labels in graphics), and "knitr" (format in LaTeX code).

isolate

A character vector with words (usually abbreviations) appearing in the middle of scientific names, which are not formatted in italics.

trim

A character vectors with words appearing at the end of scientific names that are not formatted in italics, either.

italics

A logical value indicating whether the names should be italized or not.

collapse

A character value or vector used to collapse the names and passed to paste0(). If its lenght is 2, the second value will be used to connect the two last names. Note that collapse is not yet implemented for style = "expression".

id

Integer containing either a concept or a name ID.

concept

Logical value, whether id corresponds to a concept ID or a taxon usage name ID.

include_author

Logical value, whether authors of the name should be mentioned or not.

secundum

Character value indicating the column in slot taxonViews that will be mentioned as secundum (according to).

Value

A character value including format to italic font.

See also

ape::mixedFontLabel().

Examples

## Example subspecies
summary(Easplist, 363, secundum = "secundum")
#> ------------------------------ 
#> concept ID: 363 
#> view ID: 1 - African Plant Database (2012) 
#> level: subspecies 
#> parent: 362 Ludwigia adscendens (L.) H. Hara 
#> 
#> # accepted name: 
#> 363 Ludwigia adscendens ssp. diffusa (Forssk.) P.H. Raven 
#> 
#> # synonyms (3): 
#> 50037 Ludwigia stolonifera (Guill. & Perr.) P.H. Raven 
#> 52001 Jussiaea stolonifera Guill. & Perr. 
#> 53744 Jussiaea repens auct. 
#> ------------------------------

## Empty plot
plot(x = NA, xlim = c(0, 5), ylim = c(7, 1), bty = "n", xaxt = "n", xlab = "",
  ylab = "options")

## Accepted name with author
text(x = 0, y = 1, labels = print_name(Easplist, 363, style = "expression"),
  pos = 4)

## Including taxon view
text(x = 0, y = 2, labels = print_name(Easplist, 363, style = "expression",
  secundum = "secundum"), pos = 4, cex = 0.7)

## Second mention in text
text(x = 0, y = 3, labels = print_name(Easplist, 363, style = "expression",
  second_mention = TRUE), pos = 4)

## Using synonym
text(x = 0, y = 4, labels = print_name(Easplist, 50037, style = "expression",
  concept = FALSE), pos = 4)

## Markdown style
text(0, 5, labels = print_name(Easplist, 363, style = "markdown"), pos = 4)

## HTML style
text(0, 6, labels = print_name(Easplist, 363, style = "html"), pos = 4,
    cex = 0.7)

## LaTeX style for knitr
text(x = 0, y = 7, labels = print_name(Easplist, 363, style = "knitr"), pos = 4,
    cex = 0.7)