Fits a model of ancestral state reconstruction of island presence
add_asr_node_states(
phylod,
asr_method,
tie_preference = "island",
earliest_col = FALSE,
rate_model = NULL,
...
)An object of phylo4d class with tip and node data
A phylo4d object from the package phylobase containing
phylogenetic and endemicity data for each species.
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".
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 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.
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().