DAMOCLES_sim: Simulating DAMOCLES

In DAMOCLES: Dynamic Assembly Model of Colonization, Local Extinction and Speciation

Description

Simulates DAMOCLES

Usage

DAMOCLES_sim(
  phy,
  gamma_0,
  gamma_td,
  mu,
  sigma,
  psiBranch,
  psiTrait,
  z,
  phi,
  traitOpt,
  br0,
  br_td,
  nTdim,
  root.state,
  root.trait.state,
  plotit = FALSE,
  keepExtinct = FALSE
)

Arguments

phy	phylogeny in phylo format
gamma_0	initial per lineage rate of immigration (gamma)
gamma_td	time dependency in gamma
mu	per lineage rate of local extinction
sigma	probability of local (i.e. in-situ) speciation
psiBranch	phylogenetic distance at which gamma is half gamma_0
psiTrait	trait distance at which gamma is half gamma_0
z	shape of increase in gamma with increasing trait or phylogenetic distance
phi	rate of decline in gamma with distance from trait optima
traitOpt	trait value at which gamma = gamma_0
br0	Brownian rate parameter
br_td	rate of temporal decline in Brownian rate parameter
nTdim	number of independent trait dimensions
root.state	geographic state of ancestor i.e. present (1) or absent(0)
root.trait.state	trait value of ancestor
plotit	whether to plot the phylogeny and timing of immigration/local extinction events
keepExtinct	whether to retain data for extinct lineages

Value

A list of two tables. The first table contains the following columns: The first column contains the vector of tip labels in the phylogeny The last column contains the presence (1) or absence (0) of the species The second table has dimensions d x N where d is the number of trait dimensions and N is the number of species. It contains the trait values.

Author(s)

Alex L. Pigot

References

Pigot, A.L. & R.S. Etienne (2015). A new dynamic null model for phylogenetic community structure. Ecology Letters 18: 153-163.

See Also

DAMOCLES_ML DAMOCLES_loglik

Examples

#create random phylogeny
library(ape)
phy = ape::rcoal(10)
		
#run DAMOCLES		
out = DAMOCLES_sim(
  phy,
  gamma_0 = 1.5,
  gamma_td =0,
  mu = 0,
  sigma = 0,
  psiBranch = 0,
  psiTrait = 0,
  z = 10,
  phi = 0,
  traitOpt = 1,
  br0 = 0.1,
  br_td = -0.1,
  nTdim = 2,
  root.state = 1,
  root.trait.state = 0,
  plotit = FALSE,
  keepExtinct = FALSE
  )

#the output consists of a list		
patable = out[[1]] # the first element is the presence absence table
traits = out[[2]] # this is a matrix of traits values

#show presence/absence on the tree
patable$col = rep("black",dim(patable)[1])
patable$col[which(patable$state == 1)] = "red"
plot(phy,tip.col = patable$col)

DAMOCLES documentation built on Aug. 12, 2020, 5:08 p.m.