Runs a sensitivity analysis to test the influences of changing the data on the parameter estimates for the DAISIE maximum likelihood inference model

Usage

sensitivity(
  phylo,
  island_species,
  extraction_method,
  asr_method,
  tie_preference,
  island_age,
  num_mainland_species,
  verbose = FALSE
)

Arguments

phylo: A phylogeny either as a phylo (from the ape package) or phylo4 (from the phylobase package) object.
island_species: Data frame with two columns. The first is a character string of the tip_labels with the tip names of the species on the island. The second column a character string of the endemicity status of the species, either endemic or nonendemic.
extraction_method: A character string specifying whether the colonisation time extracted is the minimum time (min) (before the present), or the most probable time under ancestral state reconstruction (asr).
asr_method: A character string, either "parsimony" or "mk" determines whether a maximum parsimony or continuous-time markov model reconstructs the ancestral states at each node. See documentation in castor::asr_max_parsimony() or castor::asr_mk_model() in castor R package for details on the methods used.
tie_preference: Character string, either "island" or "mainland" to choose the most probable state at each node using the max.col() function. When a node has island presence and absence equally probable we need to decide whether that species should be considered on the island. To consider it on the island use ties.method = "last" in the max.col() function, if you consider it not on the island use ties.method = "first". Default is "island".
island_age: Age of the island in appropriate units.
num_mainland_species: The size of the mainland pool, i.e. the number of species that can potentially colonise the island.
verbose: Boolean. States if intermediate results should be printed to console. Defaults to FALSE

Value

Data frame of parameter estimates and the parameter setting used when inferring them