description_deltaprior: Generate the description for the prior specification on the...

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

Generate the description for the prior specification on the number of dispersal routes, Δ.

Description

Generate the description for the prior specification on the number of dispersal routes, Δ.

Usage

description_deltaprior(
  states_num,
  symmetry = T,
  delta_prior = c("Poisson", "Uniform", "Beta-Binomial"),
  poisson_default = T,
  poisson_lambda = 0,
  alpha_beta = 1,
  beta_beta = 1
)

Arguments

states_num	Number of discrete states of the study trait.
symmetry	Whether the specified geographic model is symmetric (true) or asymmetric (false)
delta_prior	Which of the three prior options to put on Δ, including: "Poisson": a(n offset) Poisson distribution (the default option); "Uniform": a uniform distribution between zero and the maximum Δ (when all the dispersal routes exist), and; "Beta-Binomial": a Beta-Binomial distribution.
poisson_default	Whether to specify the default Poisson prior in BEAUti.
poisson_lambda	The rate parameter (λ) of the Poisson distribution.
alpha_beta	Parameter α of the Beta-Binomial distribution.
beta_beta	Parameter β of the Beta-Binomial distribution.

Value

an R markdown paragraph describing the specified prior on the number of dispersal routes, Δ.

Examples

description_deltaprior(5L, TRUE, "Poisson", TRUE)

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