speciesByRatesMatrix: Compute species-specific rate through time trajectories

Description

Computes the mean of the marginal posterior density of speciation/extinction or phenotypic rates for equally spaced points along the root to tip path for each species

Usage

speciesByRatesMatrix(ephy, nslices, index, spex)

Arguments

ephy

an object of class bammdata

nslices

an integer number of time slices. This determines the number of equally spaced points in time at which rates are computed for each species

index

an integer or vector of mode integer indicating which posterior samples to use in the calculation. If NULL (default) all samples are used

spex

a character string. "s" (default) calculates speciation rates; "e" calculates extinction rates; "netdiv" calculates diversification rates. Ignored if ephy$type = "trait"

Value

A list with two components:
timesA vector of time points where rates were calculated
ratesA species X times matrix of rate through time trajectories

References

bamm-project.org

Examples

Run this code

data(whales, events.whales)
ed <- getEventData(whales,events.whales,burnin=0.25, nsamples=500)
ratemat <- speciesByRatesMatrix(ed, nslices = 100)

dolphins <- extract.clade(whales,140)$tip.label
plot.new()
plot.window(xlim=c(0,35),ylim=c(0,0.8))
for (i in 1:nrow(ratemat$rates)) {
	if (whales$tip.label[i] %in% dolphins) {
		lines(ratemat$times, ratemat$rates[i,], lwd=2, col=4)	
	}
	else {
		lines(ratemat$times, ratemat$rates[i,], lwd=2, col=8)
	}
}
axis(1,seq(-5,35,5))
axis(2,seq(-0.2,0.8,0.2),las=1)
mtext("Time since root",1,line=2.5)
mtext("Speciation rate",2,line=2.5)