DAISIE_SR_sim: Simulate islands with given parameters.

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

Description

This function simulates islands with given cladogenesis, extinction, Kprime, immigration and anagenesis parameters that shift at some time. Runs the function with clade-specific carrying capacity, where diversity-dependence operates only within single clades, i.e. only among species originating from the same mainland colonist.

Returns R list object that contains the simulated islands.

Usage

DAISIE_SR_sim(time, M, pars, replicates, Tpars = NULL,
  sample_freq = 25, plot_sims = TRUE, ddep = 11, ...)

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) before the shift pars[2] corresponds to mu (extinction rate) before the shift pars[3] corresponds to K (clade-level carrying capacity) before the shift. Set K=Inf for non-diversity dependence. pars[4] corresponds to gamma (immigration rate) before the shift pars[5] corresponds to lambda^a (anagenesis rate) before the shift pars[6] corresponds to lambda^c (cladogenesis rate) after the shift pars[7] corresponds to mu (extinction rate) after the shift pars[8] corresponds to K (clade-level carrying capacity) after the shift. Set K=Inf for non-diversity dependence. pars[9] corresponds to gamma (immigration rate) after the shift pars[10] corresponds to lambda^a (anagenesis rate) after the shift pars[11] corresponds to the time of shift. This is defined as time before the end of the simulation. For example, setting time = 4 and pars[11] = 1.5 will simulate with pars[1:5] from 4 to 1.5 and with pars[6:10] from 1.5 to 0.
replicates	Number of island replicates to be simulated.
Tpars	A named list containing diversification rates considering two trait states: [1]:A numeric with the per capita transition rate with state1 [2]:A numeric with the per capita immigration rate with state2 [3]:A numeric with the per capita extinction rate with state2 [4]:A numeric with the per capita anagenesis rate with state2 [5]:A numeric with the per capita cladogenesis rate with state2 [6]:A numeric with the per capita transition rate with state2 [7]:A numeric with the number of species with trait state 2 on mainland
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.
plot_sims	Default=TRUE plots species-through-time (STT) plots. It detects how many types of species are present. If only one type of species is present, STT is plotted for all species. If two types are present, three plots are produced: STT for all, STT for type 1 and STT for type 2.
ddep	= diversity-dependent model,mode of diversity-dependence ddep == 0 no diversity-dependence ddep == 1 linear dependence in speciation rate (anagenesis and cladogenesis) ddep == 11 linear dependence in speciation rate and immigration rate ddep == 3 linear dependence in extinction rate
...	Any arguments to pass on to plotting functions.

Value

Each simulated dataset is an element of the list, which can be called using [[x]]. For example if the object is called island_replicates, the 1st replicate can be called using island_replicates[[1]] Each of the island replicates is a list in itself. The first (e.g. island_replicates[[x]][[1]]) element of that list has the following components:
$island_age - the island age
Then, we have:
$not_present - the number of mainland lineages that are not present on the island
$stt_all - STT table for all species on the island (nI - number of non-endemic species; nA - number of anagenetic species, nC - number of cladogenetic species, present - number of independent colonisations present)
The subsequent elements of the list each contain information on a single colonist lineage on the island and has 4 components:
$branching_times - island age and stem age of the population/species in the case of Non-endemic, Non-endemic_MaxAge and Endemic anagenetic species. For cladogenetic species these should be island age and branching times of the radiation including the stem age of the radiation.
$stac - the status of the colonist
* Non_endemic_MaxAge: 1
* Endemic: 2
* Endemic&Non_Endemic: 3
* Non_endemic: 4
$missing_species - number of island species that were not sampled for particular clade (only applicable for endemic clades)
$type_1or2 - whether the colonist belongs to type 1 or type 2

Author(s)

Luis Valente, Albert Phillimore, and Torsten Hauffe

References

Hauffe, T., D. Delicado, R.S. Etienne and L. Valente (submitted). Lake expansion increases equilibrium diversity via the target effect of island biogeography

See Also

DAISIE_plot_sims

Examples

# Simulate 15 islands for 4 million years with a shift in immigration rate 
# at 0.195 Ma, and plot the species-through-time plot. Pool size 296. 

pars_before_shift = c(0.079, 0.973, Inf, 0.136, 0.413)
pars_after_shift = c(0.079, 0.973, Inf, 0.652, 0.413)
tshift = 0.195
island_shift_replicates = DAISIE_SR_sim(
   time = 4,
   M = 296,
   pars = c(pars_before_shift, pars_after_shift, tshift),
   replicates = 15
 )

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