paleoPhylo: Biodiversity Analyses in a Paleontological and Phylogenetic Context

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Contains a suite of functions to analyze how speciation, extinction & character change contribute to biodiversity and display these relationships graphically. The functions are designed to inform realistic models of clade evolution; examples are drawn from data on planktonic foraminifera or generated randomly. Development is ongoing; paleoPhylo currently consists of graphical tools to plot paleobiological phylogenies incorporating stratigraphic uncertainty.

Author
Thomas Ezard and Andy Purvis
Date of publication
2014-01-16 15:20:39
Maintainer
Thomas Ezard <t.ezard@soton.ac.uk>
License
GPL (>= 2)
Version
1.0-108

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Man pages

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

Files in this package

paleoPhylo/DESCRIPTION
paleoPhylo/NAMESPACE
paleoPhylo/R
paleoPhylo/R/ape2paleoPhylo.R
paleoPhylo/R/as.paleoPhylo.R
paleoPhylo/R/buildApe.R
paleoPhylo/R/collapseBranches.R
paleoPhylo/R/createBifurcate.R
paleoPhylo/R/css.R
paleoPhylo/R/drawPhylo.R
paleoPhylo/R/getXloc.R
paleoPhylo/R/prune.to.date.R
paleoPhylo/R/pruneTree.R
paleoPhylo/R/rates.within.bins.R
paleoPhylo/R/route2root.R
paleoPhylo/R/rwb.R
paleoPhylo/R/stratUnc.R
paleoPhylo/R/timeAxis.R
paleoPhylo/data
paleoPhylo/data/berggren95.rda
paleoPhylo/data/bp05.rda
paleoPhylo/data/gradstein04.rda
paleoPhylo/data/pearson93.rda
paleoPhylo/man
paleoPhylo/man/ape2paleoPhylo.Rd
paleoPhylo/man/as.paleoPhylo.Rd
paleoPhylo/man/berggren95.Rd
paleoPhylo/man/createBifurcate.Rd
paleoPhylo/man/css.Rd
paleoPhylo/man/drawPhylo.Rd
paleoPhylo/man/gradstein04.Rd
paleoPhylo/man/paleoPhylo-package.Rd
paleoPhylo/man/pearson93.Rd
paleoPhylo/man/prune.to.date.Rd
paleoPhylo/man/pruneTree.Rd
paleoPhylo/man/rwb.Rd
paleoPhylo/man/stratUnc.Rd
paleoPhylo/man/timeAxis.Rd