Biodiversity Analyses in a Paleontological and Phylogenetic Context

Documentation for package ‘paleoPhylo’ version 1.0-108

paleoPhylo-package	Biodiversity Analyses in a Paleontological and Phylogenetic Context
ape2paleoPhylo	Convert objects of class 'phylo' to class 'paleoPhylo'.
as.paleoPhylo	The 'paleoPhylo' class.
berggren95	W.A. Berggren's 1995 geologic timescale
bp05	W.A. Berggren's 1995 geologic timescale
buildApe	Create a fully bifurcating object of class 'phylo'.
collapseBranches	Prune a tree.
createBifurcate	Create a fully bifurcating object of class 'phylo'.
css	Calculate Corrected Survivorship Scores.
drawPhylo	Plot a lineage phylogeny.
getXloc	The 'paleoPhylo' class.
gradstein04	Gradstein et al.'s 2004 Geologic Time Scale.
paleoPhylo	Biodiversity Analyses in a Paleontological and Phylogenetic Context
pearson93	An example lineage phylogeny.
prune.to.date	Returns the phylogeny of the clade to some cut-off point.
pruneTree	Prune a tree.
rates.within.bins	Calculate per-lineage origination and extinction rates within a set of bins
route2root	Prune a tree.
rwb	Calculate per-lineage origination and extinction rates within a set of bins
stratUnc	Include stratigraphic uncertainty in paleoPhylo plots.
timeAxis	Plot a time axis to append to, e.g., diversity curve plots.