crude.bd.est: Crudely estimates extinction and speciation

In treats: Trees and Traits Simulations

Crudely estimates extinction and speciation

Description

Crudely estimates the extinction and speciaton rate of a tree based on geiger::bd.km and geiger::bd.ms

Usage

crude.bd.est(tree, method, ...)

Arguments

tree	a "phylo" object.
method	either "count" or "estimate". See details.
...	any additional arguments to be passed to geiger::bd.km and geiger::bd.ms.

Details

This function calculates the extinction and speciation rates using two methods:

• "estimate" estimates the rates using the algorithm from geiger::bd.km and geiger::bd.ms based on the Magallon and Sanderson 2000 method. Note that this function provides more of a "guestimate" of extinction and speciation rates which can be especially wrong with low sampling (either missing fossil or living data). This can lead to estimating erroneous negative extinction rates.

• "count" This function calculates the extinction rate as the logged number of extinction events in the tree divided by the tree age (expressed in tree age units - e.g. million years). The speciation rate is calculated as the logged number of speciation events divided by the tree age. If the input tree has no $root.time element, the speciation and extinction rate are just the number of speciation and extinction events. Although very crude this method is slightly better at handling under sampled trees.

For more accurate model base approaches see for example birthdeath or bd.ext.

Value

A "bd.params" object to be fed to treats.

Author(s)

Thomas Guillerme

References

Magallon S and MJ Sanderson. 2000. Absolute diversification rates in angiosperm clades. Evolution 55:1762-1780.

See Also

treats make.bd.params

Examples

set.seed(1)
## Generating a random tree
my_tree <- rcoal(20)
## Estimate the number of speciations and extinctions events
crude.bd.est(my_tree, method = "estimate")

## Adding a root time
my_tree$root.time <- 5
## Count the number of speciations and extinctions
## per units of time
crude.bd.est(my_tree, method = "count")

treats documentation built on June 8, 2025, 1:43 p.m.