MagallonSanderson.Rd {laser} | R Documentation |
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 |
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 DLR32@cornell.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.
fitNDR_2rate
, getTipdata
, lambda.stem.ml
, fitNDR_1rate