DAISIE_sim_min_type2: Internal function of the DAISIE simulation

In xieshu95/DAISIE_new: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Description

Internal function of the DAISIE simulation

Usage

DAISIE_sim_min_type2(
  time,
  M,
  pars,
  replicates,
  prop_type2_pool,
  verbose = TRUE
)

Arguments

time	Numeric defining the length of the simulation in time units. For examples, if an island is known to be 4 million years old, setting time = 4 will simulate the entire life span of the island; setting time = 2 will stop the simulation at the mid-life of the island.
M	Numeric defining the size of mainland pool, i.e. the number of species that can potentially colonize the island.
pars	A numeric vector containing the model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf for diversity independence. pars[4]: gamma (immigration rate) pars[5]: lambda^a (anagenesis rate) pars[6]: lambda^c (cladogenesis rate) for either type 2 species or rate set 2 in rate shift model pars[7]: mu (extinction rate) for either type 2 species or rate set 2 in rate shift model pars[8]: K (carrying capacity) for either type 2 species or rate set 2 in rate shift model, set K=Inf for diversity independence. pars[9]: gamma (immigration rate) for either type 2 species or rate set 2 in rate shift model pars[10]: lambda^a (anagenesis rate) for either type 2 species or rate set 2 in rate shift model The elements 6:10 are required only when type 2 species are included or in the rate shift model.
replicates	Number of island replicates to be simulated.
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). For DAISIE_dataprep applies only if number_clade_types = 2. In DAISIE_dataprep the default "proportional" sets the fraction to be proportional to the number of clades of distinct macroevolutionary process that have colonised the island.
verbose	In simulation and dataprep functions a logical, Default = TRUE gives intermediate output should be printed. For ML functions a numeric determining if intermediate output should be printed, Default = 0 does not print, verbose = 1 prints intermediate output of the parameters and loglikelihood, verbose = 2 means also intermediate progress during loglikelihood computation is shown.

xieshu95/DAISIE_new documentation built on March 20, 2020, 5:31 a.m.