species_to_italics: Italicise species names

In richardjtelford/ggpalaeo: ggplot2 Plots For analogue and rioja Packages

Italicise species names

Description

Italicises species names, but not modifiers such as "var."

Usage

species_to_italics(
  x,
  families = TRUE,
  modifiers = c("spp", "sp", "fo", "var", "agg"),
  postfix = c("-type", "-t"),
  etc = character(0),
  first_with_dot_only = TRUE,
  first_capital_only = TRUE,
  no_numbers = TRUE,
  no_extra_capitals = TRUE,
  not_after_capital = TRUE,
  text = TRUE
)

Arguments

x	character; one or more species names to be italicised
families	logical; should family names be italicised
modifiers	character; vector of taxonomic terms not to italicise
postfix	character; text appended to species names that should not be italicised
etc	character; vector of other words that should not be italicised
first_with_dot_only	logical;
first_capital_only	logical; if TRUE only the first word starting with a capital letter is italicised
no_numbers	logical; if TRUE any words with numbers are not italicised
no_extra_capitals	logical; if TRUE any words with capitals other than first letter are not italicised
not_after_capital	logical; if TRUE, nothing after first extra capital is capitalised
text	logical; TRUE gives output as character vector; FALSE gives list of expressions

Details

Uses various heuristics to identify which parts of the name should be italicised and which should not. Should identify authority (if present) by the presence of the capital letter. Will probably fail with informal names unless included in 'etc'.

Value

A character vector if “text' is TRUE, otherwise a list of expressions.

Examples

species_to_italics(c("Navicula spp.", "Navicula spp", "Poaceae"))
library(ggplot2)
library(dplyr)
library(tidyr)
data(SWAP, package = "rioja")
SWAP$spec %>% mutate(pH = SWAP$pH) %>%
pivot_longer(cols = -pH, names_to = "taxa", values_to = "percent") %>%
  left_join(as_tibble(SWAP$names), by = c("taxa" = "CODE")) %>%
  group_by(taxa) %>%
  filter(sum(percent > 0) > 60, max(percent) > 20) %>%
  ggplot(aes(x = pH, y = percent)) +
  geom_point() +
  facet_wrap(~TaxonName,
             labeller = as_labeller(
               species_to_italics,
               default = label_parsed))

richardjtelford/ggpalaeo documentation built on Nov. 7, 2022, 11:03 p.m.