Quantifies effects of geo/eco distance on genetic differentiation


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Documentation for package ‘BEDASSLE’ version 1.5

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BEDASSLE-package Disentangling the contributions of geographic and ecological isolation to genetic differentiation
a0_gibbs_rate Internal BEDASSLE Functions
BB_Likelihood_counts Internal BEDASSLE Functions
BB_Prior_prob_phi Internal BEDASSLE Functions
BB_Update_mu Internal BEDASSLE Functions
BB_Update_phi Internal BEDASSLE Functions
BB_Update_thetas Internal BEDASSLE Functions
BEDASSLE Disentangling the contributions of geographic and ecological isolation to genetic differentiation
calculate.all.pairwise.Fst Calculates unbiased pairwise Fst between all sampled populations
calculate.pairwise.Fst Calculates unbiased pairwise Fst between a pair of populations
Covariance The parametric covariance matrix
HGDP.bedassle.data The Eurasian subset of the HGDP dataset used in example BEDASSLE analyses
identify_invariant_loci Internal BEDASSLE Functions
Initialize.params Internal BEDASSLE Functions
Likelihood_counts Internal BEDASSLE Functions
Likelihood_thetas Internal BEDASSLE Functions
link.up.posteriors Links up multiple MCMC output objects
load_MCMC_output Internal BEDASSLE Functions
load_posterior_predictive_samples Internal BEDASSLE Functions
make.continuing.params Generates an R object containing the last parameter values of an MCMC run (to be used for a subsequent run)
MCMC Runs the Markov chain Monte Carlo with the standard (Binomial) model
mcmc.operators Operator parameters that control the operation of the MCMC
MCMC_BB Runs the Markov chain Monte Carlo with the overdispersion (Beta-Binomial) model
plot_acceptance_rate Plots the acceptance rate of a parameter across MCMC generations
plot_all_acceptance_rates Plots the acceptance rates of all parameters across MCMC generations
plot_all_joint_marginals Plots the joint marginals for all parameter pairs
plot_all_marginals Plots the marginal densities for all parameters
plot_all_phi_marginals Plot all the marginals for the phi parameters for all populations
plot_all_phi_trace Plots all the trace plots for the phi parameters for all populations
plot_all_trace Plots all the trace plots for all parameters
plot_joint_marginal Plots the joint marginal for a pair of parameters
plot_marginal Plots the marginal density of a parameter
plot_phi_marginal Plots the marginal for the phi parameter estimated in a single population
plot_phi_trace Plots the trace plot for the phi parameter estimated in a single population
plot_posterior_predictive_samples Plots posterior predictive sampling
plot_trace Plot the trace plot for a parameter
posterior.predictive.sample Generates posterior predictive samples
Prior_prob_alpha0 Internal BEDASSLE Functions
Prior_prob_alpha2 Internal BEDASSLE Functions
Prior_prob_alphaD Internal BEDASSLE Functions
Prior_prob_alphaE Internal BEDASSLE Functions
Prior_prob_beta Internal BEDASSLE Functions
Prior_prob_mu Internal BEDASSLE Functions
Shift Internal BEDASSLE Functions
simulate_allele_count_data Internal BEDASSLE Functions
transform_frequencies Internal BEDASSLE Functions
Update_a0 Internal BEDASSLE Functions
Update_a2 Internal BEDASSLE Functions
Update_aD Internal BEDASSLE Functions
Update_aE Internal BEDASSLE Functions
Update_beta Internal BEDASSLE Functions
Update_mu Internal BEDASSLE Functions
Update_thetas Internal BEDASSLE Functions