DAISIE_format_IW_full_stt: Formats clade-specific simulation output into standard DAISIE...

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

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

Description

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

Usage

DAISIE_format_IW_full_stt(island_replicates, total_time, M, verbose)

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.
total_time	Numeric defining the length of the simulation in time units.
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.

Value

List with IW DAISIE simulation output

rsetienne/DAISIE documentation built on Oct. 25, 2023, 4:32 a.m.