sim_mutualism: sim_mutualism

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

sim_mutualism

Description

Simulate mutualistic interactions over macro-evolutionary time with specified parameters.

Usage

sim_mutualism(
  total_time,
  replicates,
  mutualism_pars,
  sample_freq,
  cond_p,
  cond_a,
  return_parts = "island_parts",
  verbose
)

Arguments

total_time	Numeric. Total time for the simulation (island age)
replicates	Integer. Number of replicates to run.
mutualism_pars	List. Parameters used in the simulation.
sample_freq	Numeric. Frequency of sampling data, for plotting.
cond_p	Integer. Condition for plants (e.g., minimum number of present plant clades on the island).
cond_a	Integer. Condition for animals (e.g., minimum number of present animal clades on the island).
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
verbose	Logical. If TRUE, prints progress updates.

Value

A list containing: - island_replicates: List of island replicates from simulations. - island_segments: Formatted data for plants and animals separated. - island_total: Formatted data for plants and animals combined.

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