genieR: genieR: Inference of demographic history from phylogeny

In xiangfstats/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 genieR.Rmd.

Author(s)

Fei Xiang, Bethany Dearlove and Simon D. W. Frost.

Maintainer: Fei Xiang ([e-mail]),

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.

https://github.com/JuliaPalacios/coalsieve.

xiangfstats/GenieR documentation built on May 4, 2019, 1:06 p.m.