crude.bd.est {treats}R Documentation

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:

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")


[Package treats version 1.1 Index]