paleotree-package {paleotree}

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.

Author(s)

David W. Bapst

Maintainer: David W. Bapst <[e-mail]>

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

# 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 above!

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)