DAISIE_format_IW: Formats island-wide simulation output into standard DAISIE...

In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Formats island-wide simulation output into standard DAISIE list output

Description

Formats island-wide simulation output into standard DAISIE list output

Usage

DAISIE_format_IW(
  island_replicates,
  time,
  M,
  sample_freq = 25,
  verbose = TRUE,
  trait_pars = NULL
)

Arguments

island_replicates	List output from DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() or DAISIE_sim_min_type2() functions. Minimally, this must be a list that has as many elements as replicates. Each element must be a list with the elements island_age, not_present and stt_all. stt_all must be a data frame with the column names Time, nI, nA, nC and present.
time	Numeric defining the length of the simulation in time units. For example, 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.
sample_freq	Numeric specifing the number of units times should be divided by for plotting purposes. Larger values will lead to plots with higher resolution, but will also run slower.
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.
trait_pars	A named list containing diversification rates considering two trait states created by create_trait_pars: [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

Value

List with CS DAISIE simulation output

Examples

island_replicates <- list()
island_replicates[[1]] <- DAISIE:::DAISIE_sim_core_cr(
  time = 5,
  mainland_n = 1000,
  pars = c(2, 2, 40, 0.1, 1),
  area_pars = DAISIE::create_area_pars(
    max_area = 1,
    current_area = 1,
    proportional_peak_t = 0,
    total_island_age = 0,
    sea_level_amplitude = 0,
    sea_level_frequency = 0,
    island_gradient_angle = 0),
  hyper_pars = create_hyper_pars(d = 0.2, x = 0.1),
  nonoceanic_pars = c(0, 0)
)
formatted_island_sampled <- DAISIE:::DAISIE_format_IW(
  island_replicates = island_replicates,
  time = 5,
  M = 1000,
  sample_freq = 25,
  verbose = FALSE
)
formatted_island_full <- DAISIE:::DAISIE_format_IW(
  island_replicates = island_replicates,
  time = 5,
  M = 1000,
  sample_freq = Inf,
  verbose = FALSE
)

DAISIE documentation built on June 2, 2022, 5:07 p.m.