m_ridgelines: 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 ridgeline of (model-averaged) diversification rates in the alternative states.

Usage

m_ridgelines(
  processed_recon,
  states_names = c("00", "01", "10", "11"),
  parameter = "turnover",
  plot_as_waiting_time = FALSE,
  fill_colors = rep(NA, 4),
  line_colors = viridis(n = 4)
)

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
plot_as_waiting_time	Whether to plot the rates (FALSE, default) or their inverse (waiting times)
fill_colors	Colors for the density polygons
line_colors	Colors for the lines and points

Value

A ridgeline plot of tip-associated rates (possibly model averaged), with carpet with the individual points and summary statistics (mean +/- sd)

Examples

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

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

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