MagallonSanderson.Rd {laser}R Documentation

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

n the number of extant species in a clade
tb the stem or crown group age
eps the relative extinction rate, or mu / lambda
r the net diversification rate, r (lambda.stem.ci only)

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

Value

a list with the following components (for speciation rate estimators)

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

Author(s)

Dan Rabosky DLR32@cornell.edu

References

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

Raup, D. M. 1985. Mathematical models of cladogenesis. Paleobiology 11:42-52.

See Also

fitNDR_2rate, getTipdata, lambda.stem.ml, fitNDR_1rate


[Package laser version 2.2 Index]