tex_analysis: Combine the descriptions on different types of analyses to...

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

Combine the descriptions on different types of analyses to generate the Analysis subsection of the Methods section.

Description

Combine the descriptions on different types of analyses to generate the Analysis subsection of the Methods section.

Usage

tex_analysis(
  further_analysis = "",
  posterioranalysis_text = "",
  summarystats_text = "",
  powerposterior_text = "",
  prioranalysis_text = "",
  dcanalysis_text = "",
  format = c("HTML", "Latex", "Markdown")
)

Arguments

further_analysis	The type of analysis selected to run, including: "": regular posterior analysis; "Marginal likelihood estimation": power-posterior analysis to estimate marginal likelihood (after regular posterior analysis); "Under prior": analysis to infer the joint prior distribution, and; "Data cloning": data-cloned posterior analysis.
posterioranalysis_text	Description of the MCMC simulation inferring the posterior distribution.
summarystats_text	Description of the geographic history inference.
powerposterior_text	Description of the power-posterior analysis.
prioranalysis_text	Description of MCMC simulations where we infer the joint prior distribution.
dcanalysis_text	Description of the MCMC simulations inferring the data-cloned posterior distribution.
format	One of "HTML", "Latex", or "Markdown".

Value

paragraphs (in the selected format) describing the analyses of the study

Examples

posterioranalysis_text <- tex_posterioranalysis(1000000, 1000, 2)
summarystats_text <- tex_summarystats("Stochastic mapping (complete history, simulation-based)")
powerposterior_text <- tex_powerposterior(64, 500000, 1000, 0.3, 2)
tex_analysis(further_analysis = "Marginal likelihood estimation", posterioranalysis_text = posterioranalysis_text, summarystats_text = summarystats_text, powerposterior_text = powerposterior_text)

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