Adds visualization of regimes to a plot
regime.plot(pars, tree, cols, type = "rect", transparency = 100)A bayou formatted parameter list
A tree of class 'phylo'
A vector of colors to give to regimes, in the same order as pars$sb
Either "rect", "density" or "lines". "rect" plots a rectangle for the 95% CI for the stationary distribution of a regime. "density" varies the transparency of the rectangles according to the probability density from the stationary distribution. "lines" plots lines for the mean and 95% CI's without filling them.
The alpha transparency value for the maximum density, max value is 255.