description_muprior: 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 average dispersal rate, μ.

Description

Generate the description for the prior specification on the average dispersal rate, μ.

Usage

description_muprior(
  mu_prior = c("CTMC rate-ref (BEAST default)", "Hierarchical Exponential",
    "Empirical-Informed Exponential"),
  tree_length = 1,
  tree_num = 1L,
  hierachexp_mu95interval = NULL,
  hierachexp_alphaofgamma = 0.5,
  hierachexp_dispersaleventsnummean = 1,
  hierachexp_dispersaleventsnum95interval = NULL,
  empinformed_dispersaleventsnummean = 1,
  parsimonyscore_quantile = 0.5
)

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_mu95interval	95\% prior interval of the hierarchical Exponential distribution.
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.
hierachexp_dispersaleventsnum95interval	95\% prior interval 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.
parsimonyscore_quantile	The quantile of the prior distribution of the number of dispersal events to put the parsimony score at.

Value

an R markdown paragraph describing the specified prior on the average dispersal rate, μ.

Examples

description_muprior("CTMC rate-ref (BEAST default)", 1000, 1)

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