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.

AuthorGideon Bradburd
Date of publication2014-12-04 00:30:44
MaintainerGideon Bradburd <gbradburd@ucdavis.edu>
LicenseGPL (>= 2)
Version1.5

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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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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