Available methods include
Described here
The implementation of these methods available in the fbdR
package assume that the age of all speciation and extinction events are known. Estimates of speciation and extinction can be obtained using maximum likelihood for trees and stratigraphic ranges, independently or jointly.
Available methods include
Desribed here
The latest version can be installed in R using the package devtools:
library(devtools)
install_github("rachelwarnock/fbdr")
fbdR
was designed to work with output from the simulation packages TreeSim
and FossilSim
but can be used to estiamte diversification rates using any simulated or empirical data, so long as they match the input format.
# TreeSim is available on CRAN
install.packages("TreeSim")
# FossilSim is available on GitHub
devtools::install_github("rachelwarnock/fossilsim")
# random number seed
set.seed(123)
# simulate a tree conditioned on tip number
lambda = 0.5
mu = 0.25
tips = 200
t = TreeSim::sim.bd.taxa(tips,1,lambda,mu)[[1]]
# simulate stratigraphic ranges assumming all speciation occurrs via budding
beta = 0
s = FossilSim::sim.taxonomy(t, beta)
# Estimate speciation and extinction using maximum likelihood
out = fbdR::est.bd.combined(t, s)
out$par[1] # tree based lambda
out$par[2] # tree based mu
out$par[3] # fossil based lambda
out$par[4] # fossil based mu
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