MagallonSanderson.Rd: Estimate speciation rates for crown and stem groups

Description

Esimate speciation rates under any relative extinction rate, given a crown or stem group age and a number of extant species

Usage

lambda.crown.ms01(n, tb, eps=0)
lambda.stem.ms01(n, tb, eps=0)
lambda.stem.ml(n, tb, eps=0)
lambda.stem.ci(tb, r, eps=0)

Arguments

the number of extant species in a clade

the stem or crown group age

eps

the relative extinction rate, or mu / lambda

the net diversification rate, r (lambda.stem.ci only)

Value

lambda: the estimated speciation rate
r: the net diversification rate
upper: upper bound of 95 percent confidence interval on expected species diversity
lower: lower bound of 95 percent confidence interval on expected diversity

Details

lambda.crown.ms01 estimates speciation rates assuming some value of eps and a crown group age after Magallon & Sanderson (2001), eqn A7.

lambda.stem.ms01 estimates speciation rates assuming a known stem clade age. Same as eqn A6 in Magallon & Sanderson 2001.

lambda.stem.ml finds maximum likelihood estimate of speciation rate given stem age and eps. This is given in Magallon & Sanderson (2001), eqns 1-2, Raup (1985) eqn A18, and others.

lambda.stem.ci gives 95 percent confidence intervals on expected species diversity after tb time units given net diversification rate r and eps

References

Magallon, S., and M. J. Sanderson. 2001. Absolute diversification rates in angiosperm clades. Evolution 55:1762-1780.