h_scatterplot: Plot diversification rates estimated by a HiSSE model (HiSSE,...

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

Description

A function to plot a scatterplot of (model-averaged) diversification rates in the alternative states. We can change the rate plotted on the y axis and modify the label for the x-axis (your binary 0/1 trait).

Usage

h_scatterplot(
  processed_recon,
  parameter = "turnover",
  states_names = c("0", "1"),
  colors = c("yellow", "violet"),
  plot_as_waiting_time = FALSE
)

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
colors	Colors for the points in the two alternate states
plot_as_waiting_time	Logical. Whether to plot the rates or their inverse (waiting times)

Value

A jittered scatterplot of (model averaged) tip-associated rates.

Examples

data("diatoms")
processed_hisse <- h_process_recon(hisse_recon=diatoms$cid4_recon)
hisse_rates_plot <- h_scatterplot(
 processed_recon=processed_hisse,
 parameter="turnover")

# modifications are easy with ggplot
# change x axis tick labels
hisse_rates_plot +
 scale_x_discrete(breaks=c(0,1), labels=c("plankton", "benthos"))

# change the position of the legend
hisse_rates_plot +
 scale_x_discrete(breaks=c(0,1), labels=c("plankton", "benthos")) +
 theme(legend.position="top")

# use expressions (for greek letters) in the axis labels
hisse_rates_plot +
 scale_x_discrete(breaks=c(0,1), labels=c("plankton", "benthos")) +
 theme(legend.position="top") +
 labs(y=expression(paste(tau, "=", lambda, "+", mu))) +
 theme(axis.text.y=element_text(size=15))

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