magsand: Estimate speciation rates for crown and stem groups

Description Usage Arguments Details Value Author(s) References See Also

Description

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

Usage

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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

or, for lambda.stem.ci

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 [email protected]

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

lambda.stem.ml


laser documentation built on Jan. 15, 2017, 4:49 p.m.