pbd_numspec_mean_checked: Calcates the mean number of species under protracted...

In richelbilderbeek/becosys: Unified Interface To Phylogenetics Models Of Speciation

Description

Calcates the mean number of species under protracted birth-death model of diversification. This is a checked version with a more explicit interface than pbd_numspec_mean.

Usage

pbd_numspec_mean_checked(ergs, eris, scrs, sirs, crown_ages)

Arguments

ergs	one or more good species' extinction rates
eris	one or more incipient species' extinction rates
scrs	one or more speciation completion rates
sirs	one or more speciation initiation rates. This function assumes the speciation initiation rates of good and incipient species are equal.
crown_ages	one or more crown ages

Value

The expected number of representative species

Author(s)

Richel J.C. Bilderbeek

See Also

pbd_numspec_mean provides for setting a time-dependence in the parameters and/or specify a stem age. pbd_numspec_median_checked calculates the median number of species.

Examples

  n <- pbd_numspec_mean_checked(
    ergs = 0.1,
    eris = 0.2,
    scrs = 0.3,
    sirs = 0.4,
    crown_ages = 0.5
  )
  testthat::expect_equal(n, 1.029111871)

  n <- pbd_numspec_mean_checked(
    ergs = 0.2,
    eris = 0.4,
    scrs = 0.6,
    sirs = 0.8,
    crown_ages = 1.0
  )
  testthat::expect_equal(n, 1.440746567)

  # Vectorized use
  ns <- pbd_numspec_mean_checked(
    ergs = c(0.1, 0.2),
    eris = c(0.2, 0.4),
    scrs = c(0.3, 0.6),
    sirs = c(0.4, 0.8),
    crown_ages = c(0.5, 1.0)
  )
  testthat::expect_equal(ns, c(1.029111871, 1.440746567))

richelbilderbeek/becosys documentation built on Oct. 19, 2020, 9:20 a.m.