Fit a constant-rate birth-death process to a phylogeny

fitCRBD fits a constant-rate birth-death process to a phylogeny in the format of ape package's phylo object. Optimization is based on likelihood functions made with diversitree. This function is basically a wrapper for the diversitree's make.bd function.

Usage

fitCRBD(phy, n.opt = 5, l.min = 0.001, l.max = 5, max.bad = 200)

Arguments

phy

A phylo object, following terminology from package ape, in which function will operate.

n.opt

Number of optimizations that will be tried by function.

l.min

Lower bound for optimization. Default value is 0.001.

l.max

Upper bound for optimization. Default value is 5.

max.bad

Maximum number of unsuccessful optimization attempts. Default value is 200.

Value

A numeric with the best estimates of speciation S and extinction E rates.

References

Paradis, E. (2012). Analysis of Phylogenetics and Evolution with R (Vol. 2). New York: Springer.

Popescu, A. A., Huber, K. T., & Paradis, E. (2012). ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R. Bioinformatics, 28(11), 1536-1537.

FitzJohn, R. G. (2010). Analysing diversification with diversitree. R Package. ver, 9-2.

FitzJohn, R. G. (2012). Diversitree: comparative phylogenetic analyses of diversification in R. Methods in Ecology and Evolution, 3(6), 1084-1092.

See also

see help page from diversitree::make.bd and stats::optim

Other macroevolution: calcFossilDivTT(), checkAndFixUltrametric(), countSeqDiffs(), estimateSpeciation(), lttPlot(), plotPaintedWhales(), plotProteinSeq(), plotRawFossilOccs(), simulateBirthDeathRich(), simulateTree()

Author

Daniel Rabosky, Matheus Januario, Jennifer Auler

Examples

S <- 0.1
E <- 0.1
set.seed(1)
phy <- simulateTree(pars = c(S, E), max.taxa = 30, max.t = 8)
fitCRBD(phy)
#>         S         E 
#> 0.2471886 0.6915988