phylodyn-package: Tools for analyzing genealogy and genome sequence data using...

In phylodyn: Statistical Tools for Phylodynamics

Description

Tools for analyzing genealogy and genome sequence data using INLA and MCMC.

Author(s)

Michael Karcher, Julia Palacios, Shiwei Lan, Vladimir Minin

Maintainer: Michael Karcher <[e-mail]>

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.

See Also

INLA

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")
}

phylodyn documentation built on May 29, 2017, 1:28 p.m.