rwb: Calculate per-lineage origination and extinction rates within...

In paleoPhylo: Biodiversity Analyses in a Paleontological and Phylogenetic Context

Description

Takes any object of class paleoPhylo and computes per-lineage origination and extinction rates within the set of bins specified by the user. Lineages persisting to the specified end are not considered to have gone extinct. Events taking place exactly on bin boundaries are taken to occur in the later bin.

Usage

rwb(pP, bL=1, st=max(pP$st), en=min(pP$en))

Arguments

pP	An object of class 'paleoPhylo' (see as.paleoPhylo).
bL	The length of bin; defaults to 1.
st	Start date for binning; defaults to start of the as.paleoPhylo object.
en	End date for binning; defaults to end of the as.paleoPhylo object.

Details

Can be used to calculate time-series of rates for correlation analysis, etc. The function identifies lineages that do something at or after the start of the bin, but before the end of the bin, meaning that lineages surviving to the specified end time are not viewed as having gone extinct)

rates.within.bins does the same thing, with slightly different variable names. This function is intended to be a faster replacement, but both are currently (version 1.0-80) still in the package. The big change is in the usage order; in rates.within.bins() it is pP, begin, end, bin.length)

Value

rwb is a data.frame, containing the following columns:

binStart	The start date of the bin.
nStart	Number of extant lineages present at the start of the bin.
branchLength	The branch length of the phylogeny within the bin.
orig	The number of originations in the bin.
extn	The number of extinctions in the bin.
lambda	Speciation rate across the bin.
mu	Extinction rate across the bin.

Author(s)

Thomas H.G. Ezard and Andy Purvis [e-mail]

References

Ezard, T.H.G. & Purvis, A. (2009). paleoPhylo: free software to draw paleobiological phylogenies. Paleobiology 35, 460-464. doi: 10.1666/0094-8373-35.3.460.

See Also

rates.within.bins, as.paleoPhylo, pearson93

Examples

data(pearson93)
p93 <- with(pearson93, as.paleoPhylo(Code, Parent, Start, End, label=Name))

p93RWB <- rwb(p93, bL=5)
with(p93RWB, plot(-binStart, lambda, col=4, lwd=2, type='l',
  xlab="Start of bin (ma)", ylab="Rate", axes=FALSE))
with(p93RWB, lines(-binStart, mu, col=2, lwd=2))
axis(1, at=seq(-65,-25,5), label=abs(seq(-65,-25,5)))
axis(2, at=seq(0,0.25,.05))

paleoPhylo documentation built on May 2, 2019, 6:11 p.m.