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Check the scientific names in the text

Source: R/species_text.R
check_species_text.Rd

Reads the manuscript – every section, the captions of the figures and tables, the supplement – and reports, with the file and the line, every scientific name not written the way journals ask.

Usage

check_species_text(
  authority = TRUE,
  abbreviate = TRUE,
  exclude = NULL,
  quiet = FALSE,
  path = NULL
)

Arguments

authority

TRUE (the default) asks for the authority at the first mention of each species in the main text. FALSE for a journal that does not want it, or gives the authorities in a table.

abbreviate

TRUE (the default) asks for the genus abbreviated after the first mention. FALSE for a journal that writes names in full every time.

exclude

Pairs of words that look like a name and are not one, or names to leave alone: "Pinus pinea".

quiet

TRUE returns what it found without printing it.

path

The project, or any folder inside it. Left out, the one set_paper() named; with none named, this stops before writing: it writes into the project, and easypaper never takes the working directory for it.

Value

A data frame, invisibly when printed, with one row per thing to look at: file, line, name as it is written, problem, and fix, what to write instead. The species found are its species attribute.

Details

What they ask for:

  • In italics, the genus and the epithet, abbreviated or not, and a genus on its own (Formica); sp. and spp. in roman (Formica spp.).

  • In full the first time (Formica rufa), and abbreviated after that (F. rufa) – except at the start of a sentence, which never opens with an abbreviation, and when two genera of the text share the initial (Formica, Fagus), where F. would not say which. Headings and captions, which are read on their own, may give the name in full.

  • With its authority the first time in the main text: Formica rufa Linnaeus, 1761, or (Linnaeus, 1761) for a species moved to another genus. The authority GBIF gives is suggested.

The abstract, the main text and the supplement are read as three documents, as a reader meets them: a name is given in full at its first mention in each. The title is only checked for italics.

Nothing is changed: whether a name in full there is a slip or a choice – a sentence that compares two species of the same genus – is yours to say. Nothing calls it either: it runs when you call it, never in a render.

How names are recognised

A pair of words shaped like a genus and an epithet is a name when GBIF lists the species, or – when it is in italics somewhere in the text – its genus and its epithet. An abbreviation (F. rufa) is a name when it abbreviates one of those, or GBIF knows its epithet. What GBIF said is kept in references/species_cache.rds, the cache of check_species(), so only new names need a connection. Without one, the cache answers, a pair already in italics is taken for a name, and a warning says what could not be checked.

See also

check_species(), for the names in the reference list.

Examples

dir <- file.path(tempdir(), "my_paper")
create_paper(dir, git = FALSE)
#> Project created: /tmp/Rtmp92gqjt/my_paper
#>   1. open my_paper.Rproj
#>   2. library(easypaper)
#>   3. set_paper(".")      # the project to work on, once a session
#>   4. render_html()      # see ?render for every command
writeLines(c("Colonies of Formica rufa were sampled.", "",
             "*Formica rufa* builds mounds."),
           file.path(dir, "_sections", "02_introduction.qmd"))
# Offline: only the cache answers, and the pair in italics is taken for a
# name. Online, GBIF is asked once for each new name.
old <- options(easypaper.species_offline = TRUE)
suppressWarnings(check_species_text(path = dir))
#> Scientific names in the text: Formica rufa
#> 2 things to look at:
#>   _sections/02_introduction.qmd:1  Formica rufa  not in italics -> *Formica rufa*
#>   _sections/02_introduction.qmd:1  Formica rufa  first mention without its authority -> Formica rufa Author, year
options(old)
unlink(dir, recursive = TRUE)