sim_core_mutualism: sim_core_mutualism

In Yangshen0325/specmutual: Evolution of Mutualism Based on Speciation, Immigration and Extinction

sim_core_mutualism

Description

This internal function runs a Monte Carlo simulation to model the dynamics of mutualistic relationships between plant and animal species on the island. The simulation tracks species interactions over time based on defined parameters and generates an island state table reflecting species composition, colonization events, and other relevant metrics. The function requires a set of parameters ('mutualism_pars') that define the initial conditions and rules governing interactions, such as colonization rates and species dynamics. It returns a comprehensive list containing the final state of the island, including species status, interaction matrices, and an evolution table documenting significant events throughout the simulation.

Usage

sim_core_mutualism(total_time, mutualism_pars, return_parts)

Arguments

total_time	Numeric. Total time for the simulation.
mutualism_pars	List. Parameters used in the simulation.
return_parts	Character. Specifies which part of the result to return. Options are: - '"island_parts"' (default): Returns only the core simulation results, including the following elements: - 'Mt': A matrix representing the "false" matrix on the island, including extinct and non-immigrated species occupying their original indices from the mainland. - 'M_true_list': A list of "true" matrices left on the island (every certain ages). - 'status_p': A one column matrix indicating the presence of the plant species on the island (Presence (1) or absence (0)). - 'status_a': A one column matrix indicating the presence of the animal species on the island (Presence (1) or absence (0)). - 'island_spec': DAISIE-alike data frame. A table showing the evolutionary trajectory of species on the island, including their colonization and branching details. - 'island': DAISIE-alike island information. A list containing three components: 'stt_table', 'clades_info_plant', and 'clades_info_animal'. - 'evo_table': A data frame summarizing the evolutionary history of the species, including branching times and other evolutionary metrics. - '"additional_parts"': Returns only additional information,for checking the rates and species richness. It contains: - 'rates_list': A list containing all types of rates - 'timeval_list': A list containing all values of time - 'richness_p_list': A list containing all plant richness on the island across simulation time - 'richness_a_list': A list containing all animal richness on the island across simulation time

Details

Internal function of simulation

Value

A list

Yangshen0325/specmutual documentation built on Feb. 19, 2025, 10:36 p.m.