simTraitsIndividuals: Simulate traits

In thauffe/TraitGmyc: What the package does (short line)

Description

This function simulates traits for a given number of individuals per species and the population size for the species

Usage

simTraitsIndividuals(
  Tree,
  Ntraits = 1,
  IndPop,
  PopFluc = NULL,
  GenLength = 1,
  Sigma2 = NULL,
  Cor = NULL,
  Alpha = NULL,
  Scenario = "A",
  TraitModel = "BM"
)

Arguments

Tree	The species tree
Ntraits	Number of traits to simulate
IndPop	Matrix or data.frame with the number of individuals per species in the first column and the species' population size in the second column. This element is returned by simGenealogy ('Species').
PopFluc	Optional matrix or data.frame with the parameters for a fluctuating population size (returned as third element form simGenealogy)
Sigma2	Optional Brownian motion rate for trait evolution. Vector of length one (the same for all traits and species) or a seperate rate per species.
Cor	Optional correlation strength between traits in the range -1,1. Either a vector of length one (same strength between all traits) or Ntraits*(Ntraits-1)/2.
Alpha	Optional strength of pull towards the morphological optima. Only effective for scenarios A, B and C. If not specified, optima is (theoretically) reached after half of the tree depth.
TraitModel	Model of trait evolution. Ether Brownian motion (BM) or Orenstein-Uhlenbeck (OU).
GenLen	Optional vector of length one for generation length (the same for all species)

Value

A matrix with traits in columns and names of individuals per species as rownames

Author(s)

Torsten Hauffe

References

Fujisawa, T. and T. Barraclough (2013): Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets. Systematic Biology 62(5), 707-724.

thauffe/TraitGmyc documentation built on July 4, 2021, 7:37 a.m.