lynchD: Compute Lynch's Delta rate metric

In paleoTS: Analyze Paleontological Time-Series

Compute Lynch's Delta rate metric

Description

This function computes D, the rate metric proposed by Lynch (1990). This metric derives from the random walk model, with D = Vstep/(2Vp), where Vstep is the step variance of the unbiased random walk, and Vp is the within sample variance, pooled among samples. Under mutation - drift equilibrium, D is expected to range approximately between 5e-5 and 5e-3.

Usage

lynchD(y, gen.per.t = 1e+06, pool = TRUE, method = c("Joint", "AD"), ...)

Arguments

y	a paleoTS object
gen.per.t	the number of generations per unit time
pool	logical, whether variances should be pooled over samples
method	parameterization to use: based on ancestor-descendant (AD) differences, or Joint consideration of all samples
...	further arguments, passed to opt.URW or opt.joint.URW

Value

D	value of rate metric
pooled.var	value of pooled within-sample variance
gen.per.t	number of generations per unit time
vstep	computed Vstep, at the original time scale of y
drift.range	expected minimum and maximum values of D consistent with neutral evolution
result	conclusion reached about the plausibility of neutral evolution

References

Lynch (1990). The rate of morphological evolution in mammals from the standpoint of the neutral expectation. The American Naturalist 136:727-741. Hunt, G. 2012. Fitting and comparing models of phyletic evolution: random walks and beyond. Paleobiology 38:351-373.

Examples

y <- sim.GRW(ns = 20, ms = 0, vs = 1e-4, tt=seq(0, 1e6, length.out=20))  # per-year simulation
lynchD(y, gen.per.t = 1)

paleoTS documentation built on Sept. 11, 2024, 9:18 p.m.