Diversification rate

Background

The funcion tree_bdestimates diversification and speciation rates evaluating uncertainty in tree topology. It estimates net diversification rate using geiger::bd.ms Magallon and Sanderson (2000) method or speciation rate using geiger::bd.km Kendall-Moran method for n trees, randomly picked from a multiPhylo file.

Examples:

1. To estimate diversification rate with Magallon and Sanderson method

library(sensiPhy)
# Load data:
data("primates")
# Run analysis
fit.ms <- tree_bd(phy = primates.phy, n.tree = 30, method = "ms")
# Check results
summary(fit.ms)
# Plot data
sensi_plot(fit.ms)

sensi_plot(fit.ms)

2. To estimate speciation rate Kendall-Moran method

# Load data:
data("primates")
# Run analysis
fit.km <- tree_bd(phy = primates.phy, n.tree = 30, method = "km")
# Check results
summary(fit.km)
# Plot data
sensi_plot(fit.km)

sensi_plot(fit.km)