sim_MCBD: Simulation of macroevolutionary diversification under the...

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

Simulation of macroevolutionary diversification under the integrated model described in Aristide & Morlon 2019

Description

Simulates the joint diversification of species and a continuous trait, where changes in both dimensions are interlinked through competitive interactions.

Usage

sim_MCBD(pars, root.value = 0, age.max = 50, step.size = 0.01, bounds = c(-Inf,Inf),
         plot = TRUE, ylims=NULL, full.sim = FALSE)

Arguments

pars	Vector of simulation parameters: pars[1] corresponds to lambda1, the speciation intitation rate pars[2] corresponds to tau0, the basal speciation completion rate pars[3] corresponds to beta, the effect of trait differences on the speciation completion rate pars[4] corresponds to mu0, the competitive extinction parameter for good species pars[5] corresponds to mubg, the background good species extinction rate pars[6] corresponds to mui0, the competitive extinction parameter for incipient species pars[7] corresponds to muibg, the background incipient species extinction rate pars[8] corresponds to alpha1, the competition effect on extinction (competition strength) pars[9] corresponds to alpha1, the competition effect on trait evolution (competition strength) pars[10] corresponds to sig2, the variance (rate) of the Brownian motion pars[11] corresponds to m, the relative contribution of character displacement (competition) with respect to stochastic (brownian) evolution
root.value	the starting trait value
age.max	maximum time for the simulation (if the process doesn't go extinct)
step.size	size of each simulation step
bounds	lower and upper value for bounds in trait space
plot	logical indicating wether to plot the simulation
ylims	y axis (trait values) limits for the simulation plot
full.sim	logical indicating wether to return the full simulation (see details)

Details

It might be difficult to find parameter combinations that are sensitive. It is recommended to use the parameter settings of the examples as a staring point and from there modify them to understand the behaviour of the model. If trees produced are too big, simulation can become too slow to ever finish.

Value

returns a list with the following elements:

all contains the complete tree of the process (extant and extinct good and incipient lineages) and trait values for each tip in the tree

gsp_fossil contains the extant and extinct good species tree and trait values for each tip in the tree

gsp_extant contains the reconstructed (extant only) good species tree and trait values for each tip in the tree

If full.sim = TRUE, two additional elements are returned inside all:

note: both elements are used internally to keep track of the simulation and are dynamically updated, so returned elements only reflect the last state

lin_mat a matrix with information about the diversification process. Each row represents a new lineage in the process with the following elements: - Parental node, descendent node (0 if a tip), starting time, ending time, status at end (extinct(-2); incipient(-1); good(1)), speciation completion or extinction time; speciation completion time (NA if still incipient).

trait_mat a list with trait values for each lineage at each time step throghout the simulation. Each element is a vector composed of the following: Lineage number (same as row number in lin_mat), status (as in lin_mat), sister lineage number, trait values (NA if lineage didn't exist yet at that time step)

Author(s)

Leandro Aristide ([e-mail])

References

Aristide, L., and Morlon, H. 2019. Understanding the effect of competition during evolutionary radiations: an integrated model of phenotypic and species diversification

Examples

lambda1 = 0.25
tau0 = 0.01
beta = 0.6
mu0 = 0.5
mubg = 0.01
mui0 = 0.8
muibg = 0.02
alpha1 = alpha2 = 0.04
sig2 = 0.5
m = 20

pars <- c(lambda1, tau0, beta, mu0, mubg,mui0, muibg, alpha1, alpha2, sig2, m)


if(test){

#1000 steps, unbounded
res <- sim_MCBD(pars, age.max=10, step.size=0.01) 

#asymmetric bounds
res <- sim_MCBD(pars, age.max=10, step.size=0.01, bounds=c(-10,Inf)) 

#only deterministic component
pars <- c(lambda1, tau0, beta, mu0, mubg, mui0, muibg, alpha1, alpha2, sig2=0, m)
res <- sim_MCBD(pars, age.max=10)

plot(res$gsp_extant$tree)

}

hmorlon/PANDA documentation built on April 24, 2024, 3:27 a.m.