m_rate_recon: Plot MuHiSSE model-averaged marginal ancestral state...

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

Description

A function to plot a (model-averaged) marginal ancestral reconstruction for the estimated diversification rates.

Usage

m_rate_recon(
  processed_recon,
  show_tip_labels = FALSE,
  parameter = "turnover",
  discrete = FALSE,
  breaks = seq(0.3, 0.6, 1),
  colors = c("red", "blue", "orange", "green"),
  plot_as_waiting_time = FALSE,
  tree_layout = "rectangular",
  tree_direction = "right",
  time_axis_ticks = 10,
  open_angle = 10
)

Arguments

processed_recon	An object produced by h_process_recon
show_tip_labels	Logical, whether to plot tip labels. Default is FALSE because it is difficult to plot legible tip labels for larger trees common in this type of analysis. See ?m_trait_recon for a good manual solution.
parameter	The diversification parameter to be mapped onto the tree. Possible options are turnover, extinct.frac, net.div, speciation, extinction
discrete	Logical. Whether to discretize the distribution of reconstructed rates into bins
breaks	A numeric vector of cut points for binning the rates. Passed internally to cut. The function checks whether 0 and max(rate) is in this vector and adds them if not. Scale appropriatelly if plot_as_waiting_time=TRUE.
colors	Colors for the branches. If discrete=TRUE a vector of length matching the number of bins produced by the breaks. If discrete=FALSE, a vector of length two giving the min/max of a color gradient.
plot_as_waiting_time	Whether to plot the rates (FALSE, default) or their inverse (waiting times)
tree_layout	A layout for the tree. Available options are 'rectangular' (default), 'slanted', 'circular', 'fan' and 'radial'.
tree_direction	'right' (default), 'left', 'up', or 'down' for rectangular and slanted tree layouts
time_axis_ticks	numeric giving the number of ticks for the time axis (default=10)
open_angle	The degrees of empty space between the first and last tip. Only works for tree_layout = 'fan' and allows for a little more space around axis tick labels.

Value

A plot of the phylogeny with branches colored by hisse-inferred marginal ancestral states.

Examples

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

m_rate_recon(
   processed_recon = processed_muhisse,
   parameter = "extinction", discrete=FALSE)

m_rate_recon(
   processed_recon = processed_muhisse,
   parameter = "extinction", discrete=TRUE, breaks=c(0.3, 0.6, 1))

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