DAISIE_sim_with_mainland: Simulate speciation, immigration and extinction on both...

In xieshu95/Test-Trasie: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Description

Simulate speciation, immigration and extinction on both mainland and island. If there are no processes, this results in equivalent results as Valente et al., 2015.

Usage

DAISIE_sim_with_mainland(time, M, pars, replicates,
  mainland_params = NULL, divdepmodel = "CS", prop_type2_pool = NA,
  replicates_apply_type2 = TRUE, sample_freq = 25)

Arguments

time	Length of the simulation in time units. For example, if an island is know to be 4 million years old, setting time = 4 will simulate entire life span of the island; setting time = 2 will stop the simulation at the mid-life of the island.
M	The size of the mainland pool, i.e the number of species that can potentially colonize the island
pars	Contains the model parameters: pars[1] corresponds to lambda^c (cladogenesis rate) pars[2] corresponds to mu (extinction rate) pars[3] corresponds to K (clade-level carrying capacity). Set K=Inf for non-diversity dependence. pars[4] corresponds to gamma (immigration rate) pars[5] corresponds to lambda^a (anagenesis rate) pars[6] corresponds to lambda^c (cladogenesis rate) for type 2 species pars[7] corresponds to mu (extinction rate) for type 2 species pars[8] corresponds to K (clade-level carrying capacity) for type 2 species. Set K=Inf for non-diversity dependence. pars[9] corresponds to gamma (immigration rate) for type 2 species pars[10] corresponds to lambda^a (anagenesis rate) for type 2 species The elements 6:10 are optional and are required only when type 2 species are included.
replicates	Number of island replicates to be simulated.
mainland_params	parameters for simulation mainland processes. If NULL, the mainland is assumed to be static, following the assumptions of Valente et al., 2016. Else the parameters can be created by DAISIE_create_mainland_params
divdepmodel	Option divdepmodel='CS' runs model with clade-specific carrying capacity, where diversity-dependence operates only within single clades, i.e. only among species originating from the same mainland colonist. Option divdepmodel= 'IW' runs model with island-wide carrying capacity, where diversity-dependence operates within and among clades.
prop_type2_pool	Fraction of mainland species that belongs to the second subset of species (type 2). Applies only when two types of species are simulated (length(pars)=10).
replicates_apply_type2	Applies only when two types of species are being simulated. Default replicates_apply_type2 = TRUE runs simulations until the number of islands where a type 2 species has colonised is equal to the specified number of replicates. This is recommended if prop_type2_pool is small or if the rate of immigration of type two species (pars[9]) is low, meaning that more replicates are needed to achieve an adequate sample size of islands with type 2 species. Setting replicates_apply_type2 = FALSE simulates islands up to the specified number of replicates regardless of whether type 2 species have colonised or not.
sample_freq	Specifies the number of units time should be divided by for plotting purposes. Larger values will lead to plots with higher resolution, but will also run slower.

Note

This function is still a stub: mainland_params is unused and a warning is emitted if this value is non-NULL

Author(s)

Richel J.C. Bilderbeek

xieshu95/Test-Trasie documentation built on Dec. 18, 2019, 7:34 a.m.