as.paleoPhylo: The 'paleoPhylo' class.
In paleoPhylo: Biodiversity Analyses in a Paleontological and Phylogenetic Context

Description Usage Arguments Details Value Author(s) References See Also Examples

A class to contain core information on a lineage phylogeny.

1	as.paleoPhylo(nm, pn, st, en, xx=NA, label=nm, grp=NA)

`nm`	A unique identifying ID code for each species lineage.
`pn`	A unique identifying ID code for the ancestor of each species lineage. Only the root is currently permitted "NA".
`st`	The date of first appearance for each species lineage.
`en`	The date of last appearance for each species lineage.
`xx`	An optional vector of some morphological trait, for use in plotting (see `drawPhylo`). Defaults to NA, which is overwritten using `getXloc`.
`label`	An optional vector of labels, for use in annotating plots (see `drawPhylo`). Defaults to the values given for nm.
`grp`	An optional vector of groups, should different (morpho)groups wish to be denoted differently (see `as.paleoPhylo`).

Provided to ease use for various data formats. Other functions in the package work with this class to do the interesting and/or useful bits. For example: convert to a fully bifurcating tree (see createBifurcate) of class 'phylo' (see as.phylo or write.tree in the ape package) or plot lineage cladograms (see getXloc and drawPhylo).

getXloc walks iteratively through the lineage phylogeny from root to tip. It allocates positions along the x-axis for each species lineage such that when plotted (see drawPhylo), they are evenly spaced. If xx is not assigned, then getXloc is called. Alternatively, any continuous morphological trait (a mixture of positive and negative values can be accomodated) can be used. To ensure that equalities are resolved, the dates are rounded to 8 decimal places in getXloc.

An object of class 'paleoPhylo', which is a list containing the five vectors defined above.

Thomas H.G. Ezard t.ezard@soton.ac.uk

Pearson, P. N. 1993 A lineage phylogeny for the Paleogene planktonic foraminifera. Micropaleontology 39, 193-222.

pearson93, createBifurcate, drawPhylo, ape2paleoPhylo

data(pearson93)
##not-defining xx leads to evenly-spaced positions along the x-axis in drawPhylo
p93 <- with(pearson93, as.paleoPhylo(Code, Parent, Start, End, label=Name))
str(p93)