fitCRBD {evolved} | R Documentation |
Fit a constant-rate birth-death process to a phylogeny
Description
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 |
n.opt |
Number of optimizations that will be tried by function. |
l.min |
Lower bound for optimization. Default value is |
l.max |
Upper bound for optimization. Default value is |
max.bad |
Maximum number of unsuccessful optimization attempts. Default
value is |
Value
A numeric
with the best estimates of speciation S
and extinction E
rates.
Author(s)
Daniel Rabosky, Matheus Januario, Jennifer Auler
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
Examples
S <- 0.1
E <- 0.1
set.seed(1)
phy <- simulateTree(pars = c(S, E), max.taxa = 30, max.t = 8)
fitCRBD(phy)