plot.BMhybResult: Plot BMhyb result

In bomeara/bmhyd: Comparative Methods for Phylogenetic Networks

Description

Shows the plot of confidence regions with MLEs indicated (red dots) or a plot of pairs of traits together. Note that for the latter plot, it converts the sampled points to an even grid with interpolation; it sets any points with likelihood worse than ten units to just ten units worse so that you can see the colors near the area of the optimum.

Usage

## S3 method for class 'BMhybResult'
plot(
  x,
  style = "univariate",
  focal.color = "red",
  inregion.color = "black",
  outregion.color = "gray",
  gradientworst.color = "black",
  gradientbest.color = "white",
  contour.color = "red",
  contour.threshold = 2,
  nrow = NULL,
  ...
)

Arguments

x	A BMhyb object (result of a BMhyb() call)
style	Either univariate or contour
focal.color	Color for the point showing the maximum likelihood estimate
inregion.color	Color for univariate plot, points in the good region
outregion.color	Color for univariate plot, points in the bad region
gradientworst.color	Color for contour plot, color of the worst contour region
gradientbest.color	Color for contour plot, color of the best contour region
contour.color	Color showing the contour line for the best threshold
contour.threshold	What delta log likelihood to use for the best/worst threshold for the contour plot
nrow	The number of rows to plot in the grid for contour (will set it automatically if NULL)
...	Other arguments to pass to plot (for univariate only; the contour plot uses ggplot2)

bomeara/bmhyd documentation built on Nov. 11, 2021, 12:37 a.m.