speciesByRatesMatrix {BAMMtools} | R Documentation |
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.
speciesByRatesMatrix(ephy, nslices, index = NULL, spex = "s")
ephy |
An object of class |
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 |
spex |
A character string. "s" (default) calculates speciation rates;
"e" calculates extinction rates; "netdiv" calculates diversification
rates. Ignored if |
A list with two components:
times A vector of time points where rates were calculated.
rates A species X times matrix of rate through time trajectories.
Mike Grundler
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)