xml_phyloctmc: Generate the treeLikelihood block in a 'BEAST' XML file.

In jsigao/prioritree: A utility for improving phylodynamic analyses in BEAST

Generate the treeLikelihood block in a 'BEAST' XML file.

Description

Generate the treeLikelihood block in a 'BEAST' XML file.

Usage

xml_phyloctmc(
  states_dat,
  discrete_trait_name,
  rootfreq_model,
  lheat = 1,
  symmetry = T,
  complete_history = T,
  do_totalcount = T,
  do_pairwisecount = T
)

Arguments

states_dat	a data-frame object containing at least two columns: one for the name of each tip (column name specified by taxon_name), and the other for the trait state of each tip (column name specified by discrete_trait_name)
discrete_trait_name	name of the column containing tip states
rootfreq_model	XML code specifying the root-frequency model (as one of the returned value of xml_discretetraitmodel)
lheat	Number of data clones
symmetry	Whether the specified geographic model is symmetric (true) or asymmetric (false)
complete_history	Whether to perform stochastic mapping to simulate full histories of the discrete-geographic trait (default) or perform the "fast" stochastic mapping to compute the expected number of events on each branch
do_totalcount	Whether to compute the number of events among all discrete states (default true) or not.
do_pairwisecount	Whether to compute the number of events between each pair of discrete states (default true) or not.

Value

XML code specifying the treeLikelihood block

jsigao/prioritree documentation built on Jan. 9, 2023, 5:35 a.m.