tex_muprior: 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 average dispersal rate, μ, specified in the study.

Description

Generate the description (in the selected format) of the prior on the average dispersal rate, μ, specified in the study.

Usage

tex_muprior(
  mu_prior = c("CTMC rate-ref (BEAST default)", "Hierarchical Exponential",
    "Empirical-Informed Exponential"),
  tree_length = 1,
  tree_num = 1L,
  hierachexp_alphaofgamma = 0.5,
  hierachexp_dispersaleventsnummean = 1,
  empinformed_dispersaleventsnummean = 1,
  parsimony_score = 1,
  format = c("HTML", "Latex", "Markdown"),
  render_citation = T
)

Arguments

mu_prior	Which of the three prior options to put on μ, including: "CTMC rate-ref (BEAST default)": default prior recommended by BEAUti on the average dispersal rate; "Hierarchical Exponential": an exponential prior whose mean is under a hyperprior and will be inferred from the data, and; "Empirical-Informed Exponential": an exponential prior whose mean is informed by prior knowledge of the study system.
tree_length	Length of the phylogenetic tree (sum of all the branch lengths, in unit of time).
tree_num	Number of phylogenetic trees to condition on (1 when the tree is fixed).
hierachexp_alphaofgamma	Shape and rate parameter of the Gamma hyperprior of the Hierarchical Exponential prior.
hierachexp_dispersaleventsnummean	Prior mean of the number of dispersal events over the phylogeny under the Hierarchical Exponential prior.
empinformed_dispersaleventsnummean	Prior mean of the number of dispersal events over the phylogeny under the Empirical-Informed Exponential prior.
parsimony_score	Parsimony number for the discrete-geographic data given the provided tree.
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 average dispersal rate specified in the study.

Examples

tex_muprior(mu_prior = "CTMC rate-ref (BEAST default)", tree_length = 1000, tree_num = 1, parsimony_score = 500L)

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