tex_deltaprior: Generate the description (in the selected format) of the...

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

Generate the description (in the selected format) of the prior on the number of dispersal routes, Δ, specified in the study.

Description

Generate the description (in the selected format) of the prior on the number of dispersal routes, Δ, specified in the study.

Usage

tex_deltaprior(
  states_num,
  symmetry = T,
  delta_prior = c("Poisson", "Uniform", "Beta-Binomial"),
  poisson_default = T,
  poisson_lambda = 0,
  alpha_beta = 1,
  beta_beta = 1,
  format = c("HTML", "Latex", "Markdown"),
  render_citation = T
)

Arguments

states_num	Number of discrete states of the study trait.
symmetry	Whether the discrete-geographic mode is symmetric (default true) or asymmetric.
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.
format	One of "HTML", "Latex", or "Markdown".
render_citation	Whether the reference list will be rendered at the end of the methods document (default true; false when just showing the description in the HTML panel).

Value

a paragraph (in the selected format) describing the prior on the number of dispersal routes specified in the study.

Examples

tex_deltaprior(states_num = 5L, symmetry = TRUE, delta_prior = "Poisson", poisson_default = TRUE, poisson_lambda = log(2))

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