phylodyn (version 0.9.0)

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

Description

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

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")
}