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

View source: R/tex_helpr.R

tex_deltapriorR Documentation

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.