xml_clockratemodel: Generate the average dispersal rate model block in a 'BEAST'...

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

Generate the average dispersal rate model block in a 'BEAST' XML file.

Description

Generate the average dispersal rate model block in a 'BEAST' XML file.

Usage

xml_clockratemodel(
  discrete_trait_name,
  ctmc = F,
  clockrate_mean = 1,
  clockrate_mean_stochastic = T,
  clockrate_proposal_weight = 1,
  clockratemean_proposal_weight = 1,
  clockrate_mean_gammashaperate = 0.5
)

Arguments

discrete_trait_name	name of the column containing tip states
ctmc	Whether to specify the CTMC-rate reference prior (default prior recommended by BEAUti) on the average dispersal rate
clockrate_mean	Mean of the Exponential prior on the average dispersal rate (relevant when an Exponential prior is used)
clockrate_mean_stochastic	Whether the mean of the Exponential prior should be treated as a random variable with a hyperprior (default true)
clockrate_proposal_weight	Weight of the proposal on the average dispersal rate
clockratemean_proposal_weight	Weight of the proposal on the mean of the Exponential prior on the average dispersal rate
clockrate_mean_gammashaperate	Shape and rate parameter (assumed to be identical) of the Gamma hyperprior of the Hierarchical Exponential prior.

Value

XML code specifying the average dispersal rate model

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