paleotree (version 1.0)

paleotree-package: paleotree: Analyses for Paleontological Phylogenies

Description

Analyzes, time-scales and simulates phylogenies of extinct/fossil lineages. Also plots diversity curves for stratigraphic range data and phylogenies, including combinations of the those two data types.

Details

ll{ Package: paleotree Type: Package Version: 1.0 Date: 2012-01-18 License: What license is it under? } This package contains functions for analyzing sampling rates given ranges of fossil taxa, in both continuous and discrete time, functions for time-scaling phylogenies of fossil taxa and functions for simulating the fossil record in both a taxic and phylogenetic varieties and converting between these.

References

The SRC method of time-scaling will be fully described in an upcoming paper (Bapst, in prep).

See Also

This package relies extensively on the phylogenetic toolkit offered by the 'ape' package. ape

Examples

##Simulate some fossil ranges with simFossilTaxa()
##Simulate some fossil ranges with simFossilTaxa()
set.seed(444)
taxa<-simFossilTaxa(p=0.1,q=0.1,nruns=1,mintaxa=20,maxtaxa=30,maxtime=1000,nExtant=0)
#let's see what the 'true' diversity curve looks like in this case
#plot the FADs and LADs with taxicDivCont()
taxicDivCont(taxa[,3:4])

#simulate a fossil record with imperfect sampling with sampleRanges()
rangesCont<-sampleRanges(taxa,r=0.5)
#plot the diversity curve based on the sampled ranges
layout(matrix(1:2,,2))
taxicDivCont(rangesCont)

#Now let's use binTimeData() to bin in intervals of 1 time unit
rangesDisc<-binTimeData(rangesCont,int.length=1)
#plot with taxicDivDisc()
taxicDivDisc(rangesDisc)
#compare to the continuous time diversity curve

#taxa2phylo assumes we know speciation events perfectly... what if we don't?
#first, let's use taxa2cladogram() to get the 'ideal' cladogram of the taxa
cladogram<-taxa2cladogram(taxa,plot=TRUE)
#Now let's try timePaleoPhy() using the continuous range data
ttree<-timePaleoPhy(cladogram,rangesCont,type="basic",plot=TRUE)
#plot diversity curve 
phyloDiv(ttree,drop.ZLB=TRUE)

#that tree lacked the terminal parts of ranges (tips stops at the taxon FADs)
#let's add those terminal ranges back on with add.term
ttree<-timePaleoPhy(cladogram,rangesCont,type="basic",add.term=TRUE,plot=TRUE)
#plot diversity curve 
phyloDiv(ttree)