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BEDASSLE  

Quantifies Effects of Geo/Eco Distance on Genetic Differentiation
View on CRAN: Click here


Download and install BEDASSLE package within the R console
Install from CRAN:
install.packages("BEDASSLE")

Install from Github:
library("remotes")
install_github("cran/BEDASSLE")

Install by package version:
library("remotes")
install_version("BEDASSLE", "1.6.1")



Attach the package and use:
library("BEDASSLE")
Maintained by
Gideon Bradburd
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2013-07-31
Latest Update: 2022-04-10
Description:
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.
How to cite:
Gideon Bradburd (2013). BEDASSLE: Quantifies Effects of Geo/Eco Distance on Genetic Differentiation. R package version 1.6.1, https://cran.r-project.org/web/packages/BEDASSLE. Accessed 21 Nov. 2024.
Previous versions and publish date:
1.0 (2013-07-31 21:22), 1.1 (2013-09-11 20:46), 1.2 (2013-10-01 07:37), 1.3 (2014-01-25 08:07), 1.4 (2014-06-10 07:07), 1.5 (2014-12-04 00:30), 1.6 (2022-04-10 21:12)
Other packages that cited BEDASSLE R package
View BEDASSLE citation profile
Other R packages that BEDASSLE depends, imports, suggests or enhances
Complete documentation for BEDASSLE
Functions, R codes and Examples using the BEDASSLE R package
Some associated functions: BEDASSLE-internal . BEDASSLE-package . Covariance . HGDP.bedassle.data . MCMC . MCMC_BB . calculate.all.pairwise.Fst . calculate.pairwise.Fst . link.up.posteriors . make.continuing.params . mcmc.operators . plot_acceptance_rate . plot_all_acceptance_rates . plot_all_joint_marginals . plot_all_marginals . plot_all_phi_marginals . plot_all_phi_trace . plot_all_trace . plot_joint_marginal . plot_marginal . plot_phi_marginal . plot_phi_trace . plot_posterior_predictive_samples . plot_trace . posterior.predictive.sample . 
Some associated R codes: BB_Likelihood_counts.R . BB_Prior_prob_phi.R . BB_Update_mu.R . BB_Update_phi.R . BB_Update_thetas.R . Covariance.R . Initialize.params.R . Likelihood_counts.R . Likelihood_thetas.R . MCMC.R . MCMC_BB.R . Prior_prob_alpha0.R . Prior_prob_alpha2.R . Prior_prob_alphaD.R . Prior_prob_alphaE.R . Prior_prob_beta.R . Prior_prob_mu.R . Shift.R . Update_a0.R . Update_a2.R . Update_aD.R . Update_aE.R . Update_beta.R . Update_mu.R . Update_thetas.R . a0_gibbs_rate.R . calculate.all.pairwise.Fst.R . calculate.pairwise.Fst.R . identify_invariant_loci.R . link.up.posteriors.R . load_MCMC_output.R . load_posterior_predictive_samples.R . make.continuing.params.R . plot_acceptance_rate.R . plot_all_acceptance_rates.R . plot_all_joint_marginals.R . plot_all_marginals.R . plot_all_phi_marginals.R . plot_all_phi_trace.R . plot_all_trace.R . plot_joint_marginal.R . plot_marginal.R . plot_phi_marginal.R . plot_phi_trace.R . plot_posterior_predictive_samples.R . plot_trace.R . posterior.predictive.sample.R . simulate_allele_count_data.R . transform_frequencies.R .  Full BEDASSLE package functions and examples
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