getTipRates: Compute tip-specific macroevolutionary rates from 'bammdata'...

In BAMMtools: Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

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")

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':

• 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.

Author(s)

Pascal Title

See Also

Requires an object of class bammdata as obtained with getEventData.

Examples

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)

BAMMtools documentation built on Sept. 13, 2024, 1:10 a.m.