Evolution Emulator: Species Diversification under an Evolutionary Relatedness Dependent Scenario.

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