rate.estimate {geiger} | R Documentation |
rate.estimate Uses Magellon and Sanderson method to calculate net diversification rate for a clade given extant diversity and age. Associated functions crown.p and stem.p also calculate the probability of obtaining a clade with at least k species given a net diversification rate (r), extinction fraction (e), and time interval. Associated functions stem.limits and crown.limits generate confidence limits on extant diversity given a net diversification rate (r), extinction fraction (e), and time interval.
rate.estimate(time=0, n=0, phy=NULL, epsilon = 0, missing = 0, crown=TRUE, kendall.moran=FALSE) crown.p(time, r, epsilon, n) stem.p(time, r, epsilon, n) crown.limits(r, epsilon, time, prob=c(0.025, 0.975)) stem.limits(r, epsilon, time, prob=c(0.025, 0.975))
time |
Time interval; can be a vector |
n |
Number of extant species |
phy |
Phylogenetic tree; can be supplied instead of time and n. If you're using a tree then crown is automatically true. |
epsilon |
Extinction rate as a fraction of speciation rate |
missing |
Number of taxa missing from tree |
crown |
If true, time is treated as crown age; otherwise, stem age |
kendall.moran |
If true, calculates Kendall-Moran estimate of speciation rate; requires a complete phylogenetic tree |
r |
Net diversification rate, birth - death |
prob |
Range of probabilities for calculating confidence region |
rate.estimate: Returns net diversification rate r = lambda - mu, and confidence interval crown.p and stem.p: Returns the probability of obtaining a clade as big as, or bigger than, size n, given time, r, and epsilon stem.limits and crown.limits: Return confidence intervals for clade size given time, r, and epsilon
Luke J. Harmon and Chad Brock
Magallon, S. and M. J. Sanderson. 2000. Absolute diversification rates in angiosperm clades. Evolution 55:1762-1780.
data(geospiza) attach(geospiza) # Assuming no extinction rate.estimate(phy=geospiza.tree, missing=1) # Assuming high extinction rate.estimate(phy=geospiza.tree, epsilon=0.9, missing=1)