getTipRates: Compute tip-specific macroevolutionary rates from `bammdata` object

Description

Return speciation, extinction, net diversification, or Brownian motion trait rates for all species in the phylogeny from BAMM output.

Usage

getTipRates(ephy, returnNetDiv = FALSE, statistic = "mean")

Value

Returns a list with the following elements:

If ephy type is 'diversification':

lambda: A matrix of tip speciation rates with species as rows, and posterior samples as columns.
mu: A matrix of tip extinction rates with species as rows, and posterior samples as columns.
lambda.avg: A vector of average tip speciation rates, averaged with mean or median, depending on selected option for statistic. The vector is named with species names.
mu.avg: A vector of average tip extinction rates, averaged with mean or median, depending on selected option for statistic. The vector is named with species names.

If ephy type is 'diversification' and

returnNetDiv = TRUE:

netdiv: A matrix of tip net diversification rates with species as rows, and posterior samples as columns.
netdiv.avg: A vector of average tip net diversification rates, averaged with mean or median, depending on selected option for statistic. The vector is named with species names.

If ephy type is 'trait':

beta: A matrix of tip phenotypic rates with species as rows, and posterior samples as columns.
beta.avg: A vector of average tip phenotypic rates, averaged with mean or median, depending on selected option for statistic. The vector is named with species names.

Arguments

ephy: An object of class bammdata.
returnNetDiv: Logical. If TRUE, then net diversification rates are returned, if FALSE, then both speciation and extinction rates are returned. If ephy is of type trait, then this is ignored.
statistic: Determines how the average tip rates should be calculated. Can be either mean or median.

Author

Pascal Title

Examples

Run this code

data(whales, events.whales)
ephy <- getEventData(whales, events.whales, burnin=0.25, nsamples = 500)

# return a vector of average species-specific speciation rates.
meanlam <- getTipRates(ephy, returnNetDiv = FALSE,
                       statistic = 'mean')$lambda.avg
meanlam

# return a vector of median species-specific net diversification rates.
ndr <- getTipRates(ephy, returnNetDiv = TRUE,
                   statistic = 'median')$netdiv.avg

# Return mean species-specific speciation rates from all posterior 
# samples in the \code{bamm-data} object.
lam <- getTipRates(ephy, returnNetDiv = FALSE, statistic = 'mean')$lambda
rowMeans(lam)