magsand: Estimate speciation rates for crown and stem groups
In laser: Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

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

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

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)

`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)

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

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

Dan Rabosky drabosky@umich.edu.edu

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.

lambda.stem.ml

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