paleotree (version 3.3.0)

paleotree-package: paleotree: Paleontological and Phylogenetic Analyses of Evolution

Description

Analyzes, time-scales and simulates phylogenies of extinct/fossil lineages, along with calculation of diversity curves. Also fits likelihood models to estimate sampling rates from stratigraphic ranges.

Details

Package:	paleotree
Type:	Package
License:	CC0

This package contains functions for analyzing sampling rates given ranges of fossil taxa, in both continuous and discrete time, functions for a posteriori time-scaling phylogenies of fossil taxa and functions for simulating the fossil record in both taxic and phylogenetic varieties.

References

Bapst, D.W. 2012. paleotree: an R package for paleontological and phylogenetic analyses of evolution. Methods in Ecology and Evolution. 3: 803-807. doi: 10.1111/j.2041-210X.2012.00223.x

Bapst, D. W. 2013. A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa. Methods in Ecology and Evolution. 4(8):724-733.

Bapst, D. W. 2013. When Can Clades Be Potentially Resolved with Morphology? PLoS ONE. 8(4):e62312.

Bapst, D. W. 2014. Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record. Paleobiology 40(3):331-351.

See Also

This package relies extensively on the phylogenetic toolkit and standards offered by the ape package, and hence lists this package as a depends, so it is loaded simultaneously.

Examples

# NOT RUN {
# get the package version of paleotree
packageVersion("paleotree")

# get the citation for paleotree
citation("paleotree")

##Simulate some fossil ranges with simFossilRecord
set.seed(444);
record <- simFossilRecord(p = 0.1, q = 0.1, nruns = 1,
	nTotalTaxa = c(30,40), nExtant = 0)
taxa <- fossilRecord2fossilTaxa(record)
#let's see what the 'true' diversity curve looks like in this case
#plot the FADs and LADs with taxicDivCont()
taxicDivCont(taxa)

#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(1:2)
taxicDivCont(rangesCont)
#Now let's use binTimeData to bin in intervals of 10 time units
rangesDisc <- binTimeData(rangesCont,int.length = 10)
#plot with taxicDivDisc
taxicDivDisc(rangesDisc)
#compare to the continuous time diversity curve

layout(1)

#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)

# }