R/genieR-package.R

In xiangfstats/GenieR: Inference of demographic history from phylogeny

#' genieR: Inference of demographic history from phylogeny
#'
#' @description The R package genieR allows inference of demographic history from reconstructed molecular phylogenies.
#' The package provides a statistical inference based on coalescent theory for the demographic history of a population from
#' phyloginies that have been reconstructed from sampled DNA sequences. It covers a few functions designed in
#' GENIE, Pybus and Rambaut (2002).
#'
#' The inference is conducted in both the maximum likelihood approach and Bayesian approach. The package also allow
#' users to simulates coalescen and sampling times for isochronous and heterochronous data. Furthermore, users can extract
#' sorted sampling/coalescent times and sampling/coalescent lineages from a phylogenetic tree.
#'
#' We encourage users to look at \code{\link{genieR.Rmd}}.
#'
#' @docType package
#'
#' @name genieR
#'
#'
#'
#'
#'
#' @references
#'
#' Hastings, W. K. (1970). Monte Carlo Sampling Methods Using Markov Chains and Their Applications.Biometrika 57 (1): 97-109.
#'
#' Kingman, J. F. C. (1982). On the Genealogy of Large Populations. Journal of Applied Probability 19, 27-43.
#'
#' Griffiths, R., and Tavare, S. (1994). Sampling Theory for Neutral Alleles in a Varying Environment. Philosophical Transactions: Biological Sciences, 344(1310), 403-410.
#'
#' Pybus, O. G., and Rambaut, A. (2002). GENIE: Estimating Demographic History from Molecular Phylogenies. Bioinformatics 18, 1404-1405.
#'
#' \url{https://github.com/JuliaPalacios/coalsieve}.
#'
#'
#' @author Fei Xiang, Bethany Dearlove and Simon D. W. Frost.
#'
#'
#'       Maintainer: Fei Xiang (\email{xf3087@@gmail.com}),
#'
#'


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