prune.to.date: Returns the phylogeny of the clade to some cut-off point.

In paleoPhylo: Biodiversity Analyses in a Paleontological and Phylogenetic Context

Description

If passed an object of class "paleoPhylo" and a particular cutoff date, then prune.to.date returns the phylogeny of the clade to that point, either excluding (the default) or including the extinct lineages within the clade. The phylogeny is returned in two formats: paleoPhylo and phylo.

Usage

prune.to.date(pP, date, 
  prune.dead.branches=TRUE, let.speciate = FALSE, let.die = FALSE)

Arguments

pP	An object of class 'paleoPhylo' (see as.paleoPhylo).
date	A particular time in the past, to which the phylogeny is cut to.
prune.dead.branches	If TRUE, prune the whole history to date rather than only the then-extant phylogeny, i.e. do not prune the extinct lineages out. Takes precedence over let.die.
let.speciate	If TRUE, speciations at exactly the cutoff date are taken to have happened.
let.die	IF TRUE, extinctions at exactly the cutoff date are taken to have happened.

Details

Enables an event-based protocol to be implemented, through iterative application along a phylogeny.

Value

paleoPhylo.tree	The pruned tree as an object of class "paleoPhylo".
phylo.tree	The pruned tree as an object of class "phylo".

Author(s)

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

as.paleoPhylo, pearson93

Examples

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

par(mfrow=c(2,4), mar=rep(1,4), cex=0.8)
eg1 <- prune.to.date(p93, 54.3)
plot(eg1$phylo.tree, main = "Default")
eg2 <- prune.to.date(p93, 54.3, prune.dead.branches=FALSE)
plot(eg2$phylo.tree, main = "Default, keeping the dead")
eg3 <- prune.to.date(p93, 54.3, let.speciate=TRUE)
plot(eg3$phylo.tree, main="Let speciate")
eg4 <- prune.to.date(p93, 54.3, prune.dead.branches=FALSE, let.speciate=TRUE) 
plot(eg4$phylo.tree, main="Let speciate, keeping the dead")
eg5 <- prune.to.date(p93, 54.3, let.die=TRUE)
plot(eg5$phylo.tree, main = "Let die")
eg6 <- prune.to.date(p93, 54.3, prune.dead.branches=FALSE, let.die=TRUE)
plot(eg6$phylo.tree, main = "Let die, keeping the dead")
eg7 <- prune.to.date(p93, 54.3, let.speciate = TRUE, let.die=TRUE)
plot(eg7$phylo.tree, main = "Live and let die")
eg8 <- prune.to.date(p93, 54.3, prune.dead.branches=FALSE, let.speciate = TRUE, let.die=TRUE)
plot(eg8$phylo.tree, main = "Live and let die, keeping the dead")

par(mfrow=c(1,1), mar=c(5.1, 4.1, 4.1, 2.1), cex=1)
  ##RESTORE DEFAULT SETTINGS

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