Formats clade-specific simulation output into standard DAISIE list output with complete STT table

Usage

DAISIE_format_CS_full_stt(
  island_replicates,
  time,
  M,
  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.

verbose

A numeric vector of length 1, which in simulations and `DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output should be printed. For ML functions a numeric determining if intermediate output should be printed. The default: `0` does not print, `1` prints the initial likelihood and the settings that were selected (which parameters are to be optimised, fixed or shifted), `2` prints the same as `1 and also the intermediate output of the parameters and loglikelihood, while `3` the same as `2` and prints intermediate progress during likelihood computation.

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