m_dotplot: Plot diversification rates estimated by a MuHiSSE model with...

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

Description

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

Usage

m_dotplot(
  processed_recon,
  states_names = c("00", "01", "10", "11"),
  parameter = "turnover",
  colors = viridis(n = 4, option = 2, end = 0.7),
  plot_as_waiting_time = FALSE,
  bin_width = 0.1
)

Arguments

processed_recon	An object produced by m_process_recon
states_names	Translation for the character states in the order 00, 01, 10, 11 (if wanted)
parameter	The diversification parameter to be plotted on the y axis. Possible options are turnover, extinct.frac, net.div, speciation, extinction
colors	Colors for the lines and points
plot_as_waiting_time	Whether to plot the rates (FALSE, default) or their inverse (waiting times)
bin_width	The width of bins for the dotplot. Treat this as any histogram. Testing several different bin width values is recommended.

Value

A stacked dotplot of tip-associated rates (possibly model averaged) with summary statistics (mean +/- sd)

Examples

data("diatoms")
processed_muhisse <- m_process_recon(muhisse_recon=diatoms$muhisse_recon)

m_dotplot(
 processed_recon = processed_muhisse,
 parameter = "extinction",
 colors = c("#000004FF", "#57157EFF", "#C43C75FF", "#FE9F6DFF"))

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