lynchD {paleoTS} | R Documentation |
This function computes D, the rate metric proposed by Lynch (1990). This metric derives from the random walk model, with D = Vstep/Vp
, 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.
lynchD(y, gen.per.t = 1e+06, pool = TRUE, ...)
y |
a paleoTS object |
gen.per.t |
the number of generations per unit time |
pool |
logical, if the variance should be pooled across samples in estimating Vstep |
... |
further arguments, passed to opt.URW |
The gen.per.t
argument indicates the number of organismal generations for each unit of time with which the time-series y
was measured. For example, is y$tt
is measured in millions of years, and the species has annual generations, gen.per.t
would be 1e6.
Estimation of Vstep
is done on the original time scale of y
, and then the values are converted to generational time scales using gen.per.t
. This is for numerical reasons, as it avoids computations on possible very low numbers.
D |
value of rate metric |
pooled.var |
value of pooled within-sample variance |
gen.per.t |
number of generations per unit time |
vstep |
Vstep
, at the original time scale of y
drift.range |
exepcted minimum and maximum values of D consistent with neutral evoltuion |
result |
conclusion reached about the plausibility of neutral evolution |
Gene Hunt
Lynch, M. 1990. The rate of morphological evolution in mammals from the standpoint of the neutral expectation. The American Naturalist 136:727–741.
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) # 1 generation per year