Runs a sensitivity analysis to test the influences of changing the data on the parameter estimates for the DAISIE maximum likelihood inference model
sensitivity(
phylo,
island_species,
extraction_method,
asr_method,
tie_preference,
island_age,
num_mainland_species,
verbose = FALSE
)Data frame of parameter estimates and the parameter setting used when inferring them
A phylogeny either as a phylo (from the ape package) or
phylo4 (from the phylobase package) object.
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.
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).
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.
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".
Age of the island in appropriate units.
The size of the mainland pool, i.e. the number of species that can potentially colonise the island.
Boolean. States if intermediate results should be printed to console. Defaults to FALSE