phylodyn: Statistical Tools for Phylodynamics

#' Tools for analyzing genealogy and genome sequence data using INLA and MCMC.
#' 
#' @author Michael Karcher,
#' Julia Palacios,
#' Shiwei Lan,
#' Vladimir Minin
#' 
#' Maintainer: Michael Karcher <mkarcher@uw.edu>
#' 
#' @seealso \code{\link[INLA:INLA-package]{INLA}}
#' 
#' @references 1. A. Rambaut, O. G. Pybus, M. I. Nelson, C. Viboud, J. K. 
#'   Taubenberger, E. C. Holmes [The genomic and epidemiological dynamics of 
#'   human influenza A 
#'   virus](http://www.nature.com/doifinder/10.1038/nature06945). *Nature*, 
#'   453(7195): 615-619, 2008.
#'   
#'   2. J. A. Palacios and V. N. Minin. [Integrated nested Laplace approximation
#'   for Bayesian nonparametric
#'   phylodynamics](http://www.auai.org/uai2012/papers/310.pdf). In *Proceedings
#'   of the Twenty-Eighth International Conference in Uncertainty in Artificial
#'   Intelligence*, pages 726-735, 2012.
#'   
#'   3. D. Zinder, T. Bedford, E. B. Baskerville, R. J. Woods, M. Roy, M.
#'   Pascual. [Seasonality in the migration and establishment of H3N2 Influenza
#'   lineages with epidemic growth and
#'   decline](http://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-014-0272-2).
#'   *BMC Evolutionary Biology*, 14(1): 272, 2014.
#'   
#'   4. S. Lan, J. A. Palacios, M. Karcher, V. N. Minin, and B. Shahbaba [An
#'   Efficient Bayesian Inference Framework for Coalescent-Based Nonparametric
#'   Phylodynamics](http://bioinformatics.oxfordjournals.org/content/31/20/3282),
#'   *Bioinformatics*, 31(20): 3282-3289, 2015.
#'   
#'   5. M. D. Karcher, J. A. Palacios, T. Bedford, M. A. Suchard, and V. N.
#'   Minin. [Quantifying and mitigating the effect of preferential sampling on
#'   phylodynamic
#'   inference](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004789).
#'   *PLOS Computational Biology*, 12:e1004789, 2016.
#'   
#'   6. J.A Palacios, J. Wakeley,  and S. Ramachandran. [Bayesian nonparametric
#'   inference of population size changes from sequential
#'   genealogies.](http://www.genetics.org/content/early/2015/07/28/genetics.115.177980)
#'   *Genetics* Vol. 201:281-304, 2015.
#' 
#' @examples
#' library(phylodyn)
#' 
#' traj = exp_traj
#' gene = coalsim(samp_times = 0, n_sampled = 100, traj = traj)
#' 
#' if (requireNamespace("INLA", quietly = TRUE)) {
#'  res_BNPR    = BNPR(data = gene)
#' 
#'  plot_BNPR(res_BNPR, traj = traj, main="BNPR")
#' }
"_PACKAGE"