R: Quantifies Effects of Geo/Eco Distance on Genetic Differentiation

# Quantifies Effects of Geo/Eco Distance on Genetic Differentiation

## Documentation for package ‘BEDASSLE’ version 1.6.1

- DESCRIPTION file

## 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