sensitivity {DAISIEprep}

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

Description

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