Plot Profile Objects — plot.species

Plot objects of class "species_distribution" produced by species_distribution and similar functions.

# S3 method for species_distribution
plot(
  x,
  type = c("RAC", "Metacommunity"),
  ...,
  fit_rac = FALSE,
  distribution = c("lnorm", "lseries", "geom", "bstick"),
  ylog = "y",
  main = NULL,
  xlab = "Rank",
  ylab = NULL,
  palette = "Set1"
)

# S3 method for species_distribution
autoplot(
  object,
  ...,
  fit_rac = FALSE,
  distribution = c("lnorm", "lseries", "geom", "bstick"),
  ylog = TRUE,
  main = NULL,
  xlab = "Rank",
  ylab = NULL,
  pch = ggplot2::GeomPoint$default_aes$shape,
  cex = ggplot2::GeomPoint$default_aes$size
)

Arguments

x: An object.
type: The type of plot. "RAC" (Rank-abundance curve, or Whittaker plot) or "Metacommunity" to represent species abundances of each community along with those of the metacommunity.
...: Additional arguments to be passed to plot. Unused elsewhere.
fit_rac: If TRUE, estimate a theoretical distribution and fit the data with it. RAC plot only.
distribution: The distribution of species abundances. May be "lnorm" (log-normal), "lseries" (log-series), "geom" (geometric) or "bstick" (broken stick). RAC plot only.
ylog: If TRUE, the Y-axis is in log-scale. RAC plot only.
main: The title of the plot.
xlab: The label of the X-axis. RAC plot only.
ylab: The label of the Y-axis.
palette: The name of a color palette, recognized by RColorBrewer::brewer.pal. RAC plot only.
object: An object of class species_distribution.
pch: The plotting characters. See graphics::points.
cex: The character expansion (size) of the points. See graphics::points.