Description Usage Arguments Details Value Author(s) References See Also Examples
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.
1 2 | prune.to.date(pP, date,
prune.dead.branches=TRUE, let.speciate = FALSE, let.die = FALSE)
|
pP |
An object of class 'paleoPhylo' (see |
date |
A particular time in the past, to which the phylogeny is cut to. |
prune.dead.branches |
If TRUE, prune the whole history to |
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. |
Enables an event-based protocol to be implemented, through iterative application along a phylogeny.
paleoPhylo.tree |
The pruned tree as an object of class "paleoPhylo". |
phylo.tree |
The pruned tree as an object of class "phylo". |
Andy Purvis a.purvis@imperial.ac.uk
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | 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
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