plot_colonisation {DAISIEprep}

Plots a dot plot (cleveland dot plot when include_crown_age = TRUE) of the stem and potentially crown ages of a community of island colonists.

Description

Plots a dot plot (cleveland dot plot when include_crown_age = TRUE) of the stem and potentially crown ages of a community of island colonists.

Usage

plot_colonisation(island_tbl, island_age, include_crown_age = TRUE)

Arguments

island_tbl

An instance of the Island_tbl class.

island_age

Age of the island in appropriate units.

include_crown_age

A boolean determining whether the crown age gets plotted with the stem age.

Value

ggplot object

Examples

set.seed(
  1,
  kind = "Mersenne-Twister",
  normal.kind = "Inversion",
  sample.kind = "Rejection"
)
phylo <- ape::rcoal(10)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e",
                     "bird_f", "bird_g", "bird_h", "bird_i", "bird_j")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- sample(
  c("not_present", "endemic", "nonendemic"),
  size = length(phylobase::tipLabels(phylo)),
  replace = TRUE,
  prob = c(0.6, 0.2, 0.2)
)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
island_tbl <- extract_island_species(phylod, extraction_method = "min")
plot_colonisation(island_tbl, island_age = 2)