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 |