DAISIEmainland: 'DAISIEmainland': A package to simulate phylogenetic data on...

In joshwlambert/DAISIEmainland: Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics

DAISIEmainland: A package to simulate phylogenetic data on an island with the presence of mainland speciation and extinction to test the DAISIE model of island biogeography.

Description

DAISIEmainland simulates a two data sets for every island: 1) the ideal data set has the full information, 2) the empirical data set has the data as would be seen by the empirical collecting phylogenetic data in the presence of mainland dynamics.

Author(s)

Joshua W. Lambert

See Also

DAISIEmainland works in association with the package DAISIE(github.com/rsetienne/DAISIE)

Examples

# simulate data for 1 island (replicate) with mainland extinction
island <- sim_island_with_mainland(
  total_time = 1,
  m = 100,
  island_pars = c(1, 1, 10, 0.1, 1),
  mainland_ex = 0.1,
  mainland_sample_prob = 1,
  mainland_sample_type = "complete",
  replicates = 1,
  verbose = FALSE
)
# simulate data for 1 island (replicate) with incomplete sampling of known
# mainland species
island <- sim_island_with_mainland(
  total_time = 1,
  m = 100,
  island_pars = c(1, 1, 10, 0.1, 1),
  mainland_ex = 0,
  mainland_sample_prob = 0.8,
  mainland_sample_type = "unsampled",
  replicates = 1,
  verbose = FALSE
)

joshwlambert/DAISIEmainland documentation built on July 14, 2024, 5:40 p.m.