Fits a model of ancestral state reconstruction of island presence

Usage

add_asr_node_states(
  phylod,
  asr_method,
  tie_preference = "island",
  earliest_col = FALSE,
  rate_model = NULL,
  ...
)

Arguments

phylod: A phylo4d object from the package phylobase containing phylogenetic and endemicity data for each species.
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".
earliest_col: A boolean to determine whether to take the colonisation time as the most probable time (FALSE) or the earliest possible colonisation time (TRUE), where the probability of a species being on the island is non-zero. Default is FALSE.
rate_model: Rate model to be used for fitting the transition rate matrix. Can be "ER" (all rates equal), "SYM" (transition rate i–>j is equal to transition rate j–>i), "ARD" (all rates can be different), "SUEDE" (only stepwise transitions i–>i+1 and i–>i-1 allowed, all 'up' transitions are equal, all 'down' transitions are equal) or "SRD" (only stepwise transitions i–>i+1 and i–>i-1 allowed, and each rate can be different). Can also be an index matrix that maps entries of the transition matrix to the corresponding independent rate parameter to be fitted. Diagonal entries should map to 0, since diagonal entries are not treated as independent rate parameters but are calculated from the remaining entries in the transition matrix. All other entries that map to 0 represent a transition rate of zero. The format of this index matrix is similar to the format used by the ace function in the ape package. rate_model is only relevant if transition_matrix==NULL.
...: dots Allows arguments to be passed to castor::asr_mk_model() and castor::asr_max_parsimony(). These arguments must match by name exactly, see ?castor::asr_mk_model() and ?castor::asr_max_parsimony() for information on arguments.

Value

An object of phylo4d class with tip and node data

Details

The rate_model argument documentation is inherited from castor::asr_mk_model(), therefore, the last sentence about the transition_matrix argument does not apply to add_asr_node_states().