rate.estimate {geiger}R Documentation

Calculate net diversification rate with confindence limits, and test diversities

Description

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.

Usage

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))

Arguments

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

Value

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

Author(s)

Luke J. Harmon and Chad Brock

References

Magallon, S. and M. J. Sanderson. 2000. Absolute diversification rates in angiosperm clades. Evolution 55:1762-1780.

Examples


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)


[Package geiger version 1.2-14 Index]