BEDASSLE: Quantifies effects of geo/eco distance on genetic differentiation

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.

Author
Gideon Bradburd
Date of publication
2014-12-04 00:30:44
Maintainer
Gideon Bradburd <gbradburd@ucdavis.edu>
License
GPL (>= 2)
Version
1.5

View on CRAN

Man pages

BEDASSLE-internal
Internal BEDASSLE Functions
BEDASSLE-package
Disentangling the contributions of geographic and ecological...
calculate.all.pairwise.Fst
Calculates unbiased pairwise Fst between all sampled...
calculate.pairwise.Fst
Calculates unbiased pairwise Fst between a pair of...
Covariance
The parametric covariance matrix
HGDP.bedassle.data
The Eurasian subset of the HGDP dataset used in example...
link.up.posteriors
Links up multiple MCMC output objects
make.continuing.params
Generates an R object containing the last parameter values of...
MCMC
Runs the Markov chain Monte Carlo with the standard...
MCMC_BB
Runs the Markov chain Monte Carlo with the overdispersion...
mcmc.operators
Operator parameters that control the operation of the MCMC
plot_acceptance_rate
Plots the acceptance rate of a parameter across MCMC...
plot_all_acceptance_rates
Plots the acceptance rates of all parameters across MCMC...
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...
plot_all_phi_trace
Plots all the trace plots for the phi parameters for all...
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...
plot_phi_trace
Plots the trace plot for the phi parameter estimated in a...
plot_posterior_predictive_samples
Plots posterior predictive sampling
plot_trace
Plot the trace plot for a parameter
posterior.predictive.sample
Generates posterior predictive samples

Files in this package

BEDASSLE
BEDASSLE/NAMESPACE
BEDASSLE/data
BEDASSLE/data/mcmc.operators.rda
BEDASSLE/data/HGDP.bedassle.data.rda
BEDASSLE/R
BEDASSLE/R/transform_frequencies.R
BEDASSLE/R/load_MCMC_output.R
BEDASSLE/R/Update_beta.R
BEDASSLE/R/plot_posterior_predictive_samples.R
BEDASSLE/R/plot_phi_trace.R
BEDASSLE/R/Prior_prob_alpha0.R
BEDASSLE/R/a0_gibbs_rate.R
BEDASSLE/R/MCMC.R
BEDASSLE/R/load_posterior_predictive_samples.R
BEDASSLE/R/identify_invariant_loci.R
BEDASSLE/R/Update_aD.R
BEDASSLE/R/plot_marginal.R
BEDASSLE/R/Update_aE.R
BEDASSLE/R/BB_Prior_prob_phi.R
BEDASSLE/R/BB_Update_mu.R
BEDASSLE/R/BB_Likelihood_counts.R
BEDASSLE/R/Likelihood_thetas.R
BEDASSLE/R/Prior_prob_alphaE.R
BEDASSLE/R/posterior.predictive.sample.R
BEDASSLE/R/plot_all_acceptance_rates.R
BEDASSLE/R/Update_a2.R
BEDASSLE/R/Likelihood_counts.R
BEDASSLE/R/BB_Update_phi.R
BEDASSLE/R/Update_mu.R
BEDASSLE/R/plot_all_phi_trace.R
BEDASSLE/R/Prior_prob_alphaD.R
BEDASSLE/R/plot_trace.R
BEDASSLE/R/calculate.all.pairwise.Fst.R
BEDASSLE/R/make.continuing.params.R
BEDASSLE/R/plot_all_trace.R
BEDASSLE/R/MCMC_BB.R
BEDASSLE/R/simulate_allele_count_data.R
BEDASSLE/R/BB_Update_thetas.R
BEDASSLE/R/plot_all_joint_marginals.R
BEDASSLE/R/Prior_prob_mu.R
BEDASSLE/R/Update_thetas.R
BEDASSLE/R/Update_a0.R
BEDASSLE/R/plot_joint_marginal.R
BEDASSLE/R/Prior_prob_beta.R
BEDASSLE/R/Initialize.params.R
BEDASSLE/R/Covariance.R
BEDASSLE/R/link.up.posteriors.R
BEDASSLE/R/plot_acceptance_rate.R
BEDASSLE/R/plot_all_phi_marginals.R
BEDASSLE/R/Shift.R
BEDASSLE/R/plot_all_marginals.R
BEDASSLE/R/Prior_prob_alpha2.R
BEDASSLE/R/plot_phi_marginal.R
BEDASSLE/R/calculate.pairwise.Fst.R
BEDASSLE/MD5
BEDASSLE/DESCRIPTION
BEDASSLE/man
BEDASSLE/man/MCMC_BB.Rd
BEDASSLE/man/MCMC.Rd
BEDASSLE/man/calculate.pairwise.Fst.Rd
BEDASSLE/man/plot_all_acceptance_rates.Rd
BEDASSLE/man/posterior.predictive.sample.Rd
BEDASSLE/man/plot_acceptance_rate.Rd
BEDASSLE/man/plot_all_phi_marginals.Rd
BEDASSLE/man/plot_all_trace.Rd
BEDASSLE/man/plot_posterior_predictive_samples.Rd
BEDASSLE/man/BEDASSLE-package.Rd
BEDASSLE/man/mcmc.operators.Rd
BEDASSLE/man/Covariance.Rd
BEDASSLE/man/make.continuing.params.Rd
BEDASSLE/man/plot_all_phi_trace.Rd
BEDASSLE/man/plot_trace.Rd
BEDASSLE/man/plot_joint_marginal.Rd
BEDASSLE/man/plot_phi_trace.Rd
BEDASSLE/man/plot_marginal.Rd
BEDASSLE/man/BEDASSLE-internal.Rd
BEDASSLE/man/calculate.all.pairwise.Fst.Rd
BEDASSLE/man/plot_all_marginals.Rd
BEDASSLE/man/HGDP.bedassle.data.Rd
BEDASSLE/man/plot_phi_marginal.Rd
BEDASSLE/man/plot_all_joint_marginals.Rd
BEDASSLE/man/link.up.posteriors.Rd