Simulates island assemblages under known colonization, speciation, and extinction parameters

Generates a dated phylogeny and presence-absence matrix under a birth-death-colonization process with known parameters, returning both the simulated data and the true event table for use in insitu_power.

Usage

simulate_island(
  n_tips,
  birth_rate,
  death_rate = 0,
  colonization_rate,
  island_extinction_fraction = 0,
  n_islands = 1,
  seed = NULL
)

Arguments

n_tips

Total number of tips in the simulated tree.

birth_rate

Per-lineage speciation rate.

death_rate

Per-lineage extinction rate. Default: 0.

colonization_rate

Expected number of colonization events per unit of total branch length. Controls how many internal nodes are selected as colonization origins.

island_extinction_fraction

Proportion of island tips to remove at random, simulating extinction. Default: 0.

n_islands

Number of distinct islands. Colonization nodes are distributed across islands in sequence. Default: 1.

seed

Optional random seed. Default: NULL.

Value

A named list with elements phy, PAM, and true_events. true_events has the same structure as the output of map_insitu_events and serves as the ground truth for power analysis.

Details

The simulation places colonization events directly on the tree by randomly selecting internal nodes as colonization origins. The number of colonization events is drawn from a Poisson distribution with mean equal to colonization_rate multiplied by the total branch length of the tree. Tips descending from a colonization node are assigned to an island; all other tips are mainland. True in-situ events are nodes where both descendant clades share exactly one island, computed directly from the simulated topology without any ASR.