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

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

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.

Value

Returns a list with the following elements:

If ephy type is 'diversification':

If ephy type is 'diversification' and returnNetDiv = TRUE:

If ephy type is 'trait':

Author(s)

Pascal Title

See Also

Requires an object of class bammdata as obtained with getEventData.

Examples

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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)

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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