h_dotplot: Plot diversification rates estimated by a HiSSE model with...

In teofiln/utilhisse: A Collection of Functions for Summarising and Visualizing 'hisse' Results

Description

A function to plot a dotplot of (model-averaged) diversification rates in the alternative states.

Usage

h_dotplot(
  processed_recon,
  parameter = "turnover",
  states_names = c("Marine", "Freshwater"),
  bin_width = 0.1,
  colors,
  plot_as_waiting_time = TRUE
)

Arguments

processed_recon	An object produced by h_process_recon
parameter	The diversification parameter to be plotted on the y axis. Possible options are turnover, extinct.frac, net.div, speciation, extinction
states_names	A character vector of length two giving the translation for states 0 and 1.
bin_width	The width of bins for the dotplot. Treat this as any histogram. Testing several different bin width values is recommended.
colors	Colors for the points in the two alternate states
plot_as_waiting_time	Whether to plot the rates or their inverse (waiting times)

Value

A dotplot of tip-associated rates (possibly model averaged).

Examples

data("diatoms")
processed_hisse <- h_process_recon(hisse_recon=diatoms$cid4_recon)

h_dotplot(
  processed_recon = processed_hisse,
  parameter = "turnover",
  states_names = c("Plankton", "Benthos"),
  bin_width = 0.2,
  colors=c("orange", "violet"),
  plot_as_waiting_time = TRUE
) + labs(x = "", y = "Waiting time (My)", title = "Turnover")

# see ?h_scatterplot for examples for modifying the graph using ggplot2

teofiln/utilhisse documentation built on Sept. 3, 2020, 2:55 p.m.