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.

Install the latest version of this package by entering the following in R:
install.packages("BEDASSLE")
AuthorGideon Bradburd
Date of publication2014-12-04 00:30:44
MaintainerGideon Bradburd <gbradburd@ucdavis.edu>
LicenseGPL (>= 2)
Version1.5

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

Functions

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

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.