bd.ms: estimate net diversification rate

In mwpennell/geiger-v2: Analysis of Evolutionary Diversification

estimate net diversification rate

Description

estimating net diversification rate with confidence limits and testing diversities

Usage

bd.ms(phy=NULL, time, n, missing = 0, crown=TRUE, epsilon = 0)
bd.km(phy=NULL, time, n, missing = 0, crown=TRUE)
crown.p(phy=NULL, time, n, r, epsilon)
stem.p(phy=NULL, time, n, r, epsilon)
crown.limits(time, r, epsilon, CI=0.95)
stem.limits(time, r, epsilon, CI=0.95)

Arguments

phy	a phylogenetic tree of class 'phylo' (see Details)
time	time interval (can be a vector)
n	number of extant species
r	net diversification rate, birth - death
epsilon	extinction rate as a fraction of speciation rate
missing	number of taxa missing from tree
crown	whether time is treated as crown age (or otherwise as stem age)
CI	confidence level for estimated parameters

Details

bd.ms uses the Magallon and Sanderson (2000) method to calculate net diversification rate for a clade given extant diversity and age. bd.km computes the Kendall-Moran estimate of speciation rate, which assumes a complete phylogenetic tree.

Associated functions crown.p and stem.p also calculate the probability of obtaining a clade with at least n species given a net diversification rate (r), extinction fraction (epsilon), and time interval. Associated functions stem.limits and crown.limits generate confidence limits on extant diversity given a net diversification rate (r), extinction fraction (epsilon), and time interval.

Where a function calls for a time and an n element, a tree may be given instead (as argument phy). The argument n is taken from the number of tips in the tree. The method will attempt to discern whether the model should be fitted assuming crown or stem. If the tree has a non-NULL phy$root.edge element, the length will be assumed for the stem and crown is assumed to be FALSE (see also read.tree).

Value

• bd.ms returns net diversification rate (r = lambda - mu)

• bd.km returns speciation rate assuming a completely sampled tree

• crown.p and stem.p return the probability of obtaining a clade as big as (or bigger than) size n, given time, r, and epsilon

• crown.limits and stem.limits return lower (lb) and upper (ub) confidence intervals for clade size given time, r, and epsilon

Author(s)

LJ Harmon and C Brock

References

Magallon S and MJ Sanderson. 2000. Absolute diversification rates in angiosperm clades. Evolution 55:1762-1780.

Examples

geo=get(data(geospiza))

# Assuming no extinction
bd.ms(phy=geo$phy, missing=1, epsilon=0)

# Assuming high extinction
bd.ms(phy=geo$phy, missing=1, epsilon=0.9)

mwpennell/geiger-v2 documentation built on Feb. 26, 2023, 1:19 a.m.