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

Value

a list with the following components (for speciation rate estimators)
lambdathe estimated speciation rate
rthe net diversification rate
or, for lambda.stem.ci
upperupper bound of 95 percent confidence interval on expected species diversity
lowerlower 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.

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