sim_BD: Function to simulate a birth-death-fossilization process.

In josteist/Compadre: Analysis of Macroevolutionary Rates of Speciation, Extinction and Sampling using Capture-Mark-Recapture techniques

Description

This function simulates a birth-death process with a fossilization/sampling scheme. Rates of speciation and extinction can be dependent on time t and standing diversity/richness, n. Sampling rates can be dependent om time.

Usage

sim_BD(spec = 0.1, ext = 0.02, samp = 0.3, n_init = 100, dt_ints = rep(1, 10))

Arguments

spec	Speciation rate. Either given as a fixed rate or as a function of time (t) and richness (n). Defaults to 0.1.
ext	Extinction rate. Given as fixed rate or function of time and richness. Defaults to 0.001.
samp	Sampling rate, given as fixed rate or function of time (t) only. Defaults to 0.3
n_init	Initial number of lineages. Defaults to 100.
dt_ints	Array of 'intervals' in which to generate the fossil record, as an array of interval durations. All lineages sampled within these intervals are placed in the interval, regardless of precise time it was sampled for the output FosRec. Defaults to rep(1,10)

Value

A named list with Taxa (time of origin and extinction of all taxa), Foss (list of all fossilization/sampling event for all taxa), FosRec (occurrence matrix with dimensions sampled species by intervals). The remainding entries in the list are the inputs given to the function, dts, Spec, Ext, Samp, n_init

josteist/Compadre documentation built on June 3, 2021, 1:02 p.m.