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BEDASSLE (version 1.6.1)

Quantifies Effects of Geo/Eco Distance on Genetic Differentiation

Description

Provides functions that allow users to quantify the relative contributions of geographic and ecological distances to empirical patterns of genetic differentiation on a landscape. Specifically, we use a custom Markov chain Monte Carlo (MCMC) algorithm, which is used to estimate the parameters of the inference model, as well as functions for performing MCMC diagnosis and assessing model adequacy.

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Version

Install

install.packages('BEDASSLE')

Monthly Downloads

383

Version

1.6.1

License

GPL (>= 2)

Maintainer

Gideon Bradburd

Last Published

January 11th, 2024

Functions in BEDASSLE (1.6.1)

plot_all_phi_trace

Plots all the trace plots for the phi parameters for all populations

plot_all_phi_marginals

Plot all the marginals for the phi parameters for all populations

Plots the trace plot for the phi parameter estimated in a single population

plot_phi_marginal

Plots the marginal for the phi parameter estimated in a single population

posterior.predictive.sample

Generates posterior predictive samples

plot_acceptance_rate

Plots the acceptance rate of a parameter across MCMC generations

Plots all the trace plots for all parameters

Plot the trace plot for a parameter

plot_posterior_predictive_samples

Plots posterior predictive sampling

calculate.pairwise.Fst

Calculates unbiased pairwise Fst between a pair of populations

BEDASSLE-internal

Internal BEDASSLE Functions

Runs the Markov chain Monte Carlo with the standard (Binomial) model

calculate.all.pairwise.Fst

Calculates unbiased pairwise Fst between all sampled populations

Runs the Markov chain Monte Carlo with the overdispersion (Beta-Binomial) model

The parametric covariance matrix

BEDASSLE-package

Disentangling the contributions of geographic and ecological isolation to genetic differentiation

make.continuing.params

Generates an R object containing the last parameter values of an MCMC run (to be used for a subsequent run)

link.up.posteriors

Links up multiple MCMC output objects

HGDP.bedassle.data

The Eurasian subset of the HGDP dataset used in example BEDASSLE analyses

plot_joint_marginal

Plots the joint marginal for a pair of parameters

plot_all_acceptance_rates

Plots the acceptance rates of all parameters across MCMC generations

Operator parameters that control the operation of the MCMC

plot_all_joint_marginals

Plots the joint marginals for all parameter pairs

Plots the marginal density of a parameter

plot_all_marginals

Plots the marginal densities for all parameters