Quantifies Effects of Geo/Eco Distance on Genetic
Differentiation
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Documentation for package ‘BEDASSLE’ version 1.6.1
Help Pages
| 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 |