Evolution Emulator: Species Diversification under an Evolutionary Relatedness Dependent Scenario

Evolutionary relatedness dependent diversification simulation powered by the 'Rcpp' back-end 'SimTable'.

Our publication of the 'evesim' package

Tianjian Qin, Luis Valente, Rampal Etienne. Impact of evolutionary relatedness on species diversification and tree shape. Journal of Theoretical Biology. DOI: https://doi.org/10.1016/j.jtbi.2024.111992

Special thanks to Hanno Hildenbrandt and Thijs Janzen

How to install

require(remotes)
remotes::install_github("EvoLandEco/evesim")

How to use

library(evesim)
library(ape)

# Optionally set the number of threads.
# Defaults to number of logical cores.
RcppParallel::setThreadOptions(numThreads = 1)

# Simulation
# In the below example, we set speciation rate to 0.5, extinction rate to 0.1
# We also set the effect sizes of species richness and evolutionary relatedness on speciation process to -0.001 and -0.001
# In the example, the effects on extinction are set to zeros
pars = c(0.5, 0.1, -0.001, -0.001, 0.0, 0.0)

# With pre-set parameters, we now run a simulation to generate trees with crown age fixed at 10 time units
# We use the NND (nearest neighbor distance) scenario
sim <- edd_sim(pars = pars, age = 10, metric = "nnd", offset = "none")

# Simulation outputs are embedded in the 'sim' object
# Plot extant tree
plot(sim$tes)

# Plot complete tree
plot(sim$tas)

# L table (to view the evolutionary history)
sim$L