{ "_id": "6ac35fd4d743750d376db1c0", "Package": "BEDASSLE", "Type": "Package", "Title": "Quantifies Effects of Geo/Eco Distance on Genetic\nDifferentiation", "Version": "1.6.1", "Date": "2024-1-09", "Author": "Gideon Bradburd", "Maintainer": "Gideon Bradburd ", "Description": "Provides functions that allow users to quantify the\nrelative contributions of geographic and ecological distances\nto empirical patterns of genetic differentiation on a\nlandscape. Specifically, we use a custom Markov chain Monte\nCarlo (MCMC) algorithm, which is used to estimate the\nparameters of the inference model, as well as functions for\nperforming MCMC diagnosis and assessing model adequacy.", "License": "GPL (>= 2)", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-05 08:25:16 UTC", "User": "root" }, "Repository": "https://gbradburd.r-universe.dev", "Date/Publication": "2024-01-12 02:39:37 UTC", "RemoteUrl": "https://github.com/cran/BEDASSLE", "RemoteRef": "HEAD", "RemoteSha": "72da7d622fb526ee5dae40a408f5ab66f470282e", "_user": "gbradburd", "_type": "src", "_file": "BEDASSLE_1.6.1.tar.gz", "_fileid": "https://r2.ropensci.org/259ccb2901f19a8a522c7cf3c254ede6aba153c0c4e32619e704f44081cf9f94", "_filesize": 307772, "_sha256": "259ccb2901f19a8a522c7cf3c254ede6aba153c0c4e32619e704f44081cf9f94", "_expires": "2027-01-13T08:29:07.000Z", "_created": "2026-10-05T08:25:16.000Z", "_published": "2026-10-05T08:29:08.845Z", "_jobs": [ { "job": 111677013196, "time": 124, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11333591035" }, { "job": 111677013270, "time": 132, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11333860916" }, { "job": 111677013204, "time": 181, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11333341239" }, { "job": 111677013378, "time": 169, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11333511459" }, { "job": 111676006582, "time": 139, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11333101386" }, { "job": 111677013106, "time": 77, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11333321824" }, { "job": 111677013231, "time": 103, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11333910517" }, { "job": 111677013262, "time": 78, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11333590905" }, { "job": 111677013296, "time": 87, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11333676095" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/gbradburd/actions/runs/37283211148", "_status": "success", "_upstream": "https://github.com/cran/BEDASSLE", "_commit": { "id": "72da7d622fb526ee5dae40a408f5ab66f470282e", "author": "Gideon Bradburd ", "committer": "cran-robot ", "message": "version 1.6.1\n", "time": 1705027177 }, "_maintainer": { "name": "Gideon Bradburd", "email": "bradburd@umich.edu", "login": "gbradburd", "description": "", "uuid": 6391876 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "MASS", "role": "Imports" }, { "package": "matrixcalc", "role": "Imports" }, { "package": "emdbook", "role": "Imports" } ], "_owner": "cran", "_selfowned": true, "_usedby": 1, "_updates": [], "_tags": [], "_stars": 2, "_contributors": [ { "user": "gbradburd", "count": 8, "uuid": 6391876 } ], "_userbio": { "uuid": 6391876, "type": "user", "name": "Gideon Bradburd", "followers": 45 }, "_downloads": { "count": 444, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BEDASSLE" }, "_mentions": 14, "_searchresults": 30, "_rbuild": "4.6.1", "_assets": [ "extra/BEDASSLE.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf" ], "_realowner": "gbradburd", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2013-07-31" }, { "version": "1.1", "date": "2013-09-11" }, { "version": "1.2", "date": "2013-10-01" }, { "version": "1.3", "date": "2014-01-25" }, { "version": "1.4", "date": "2014-06-10" }, { "version": "1.5", "date": "2014-12-03" }, { "version": "1.6", "date": "2022-04-10" }, { "version": "1.6.1", "date": "2024-01-12" } ], "_exports": [ "a0_gibbs_rate", "BB_Likelihood_counts", "BB_Prior_prob_phi", "BB_Update_mu", "BB_Update_phi", "BB_Update_thetas", "calculate.all.pairwise.Fst", "calculate.pairwise.Fst", "Covariance", "identify_invariant_loci", "Initialize.params", "Likelihood_counts", "Likelihood_thetas", "link.up.posteriors", "load_MCMC_output", "load_posterior_predictive_samples", "make.continuing.params", "MCMC", "MCMC_BB", "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", "Prior_prob_alpha0", "Prior_prob_alpha2", "Prior_prob_alphaD", "Prior_prob_alphaE", "Prior_prob_beta", "Prior_prob_mu", "Shift", "simulate_allele_count_data", "transform_frequencies", "Update_a0", "Update_a2", "Update_aD", "Update_aE", "Update_beta", "Update_mu", "Update_thetas" ], "_datasets": [ { "name": "HGDP.bedassle.data", "title": "The Eurasian subset of the HGDP dataset used in example BEDASSLE analyses", "object": "HGDP.bedassle.data", "file": "HGDP.bedassle.data.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "mcmc.operators", "title": "Operator parameters that control the operation of the MCMC", "object": "mcmc.operators", "file": "mcmc.operators.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "BEDASSLE-package", "title": "Disentangling the contributions of geographic and ecological isolation to genetic differentiation", "topics": [ "BEDASSLE-package", "BEDASSLE" ] }, { "page": "BEDASSLE-internal", "title": "Internal BEDASSLE Functions", "topics": [ "a0_gibbs_rate", "BB_Likelihood_counts", "BB_Prior_prob_phi", "BB_Update_mu", "BB_Update_phi", "BB_Update_thetas", "identify_invariant_loci", "Initialize.params", "Likelihood_counts", "Likelihood_thetas", "load_MCMC_output", "load_posterior_predictive_samples", "Prior_prob_alpha0", "Prior_prob_alpha2", "Prior_prob_alphaD", "Prior_prob_alphaE", "Prior_prob_beta", "Prior_prob_mu", "Shift", "simulate_allele_count_data", "transform_frequencies", "Update_a0", "Update_a2", "Update_aD", "Update_aE", "Update_beta", "Update_mu", "Update_thetas" ] }, { "page": "calculate.all.pairwise.Fst", "title": "Calculates unbiased pairwise Fst between all sampled populations", "topics": [ "calculate.all.pairwise.Fst" ] }, { "page": "calculate.pairwise.Fst", "title": "Calculates unbiased pairwise Fst between a pair of populations", "topics": [ "calculate.pairwise.Fst" ] }, { "page": "Covariance", "title": "The parametric covariance matrix", "topics": [ "Covariance" ] }, { "page": "HGDP.bedassle.data", "title": "The Eurasian subset of the HGDP dataset used in example BEDASSLE analyses", "topics": [ "HGDP.bedassle.data" ] }, { "page": "link.up.posteriors", "title": "Links up multiple MCMC output objects", "topics": [ "link.up.posteriors" ] }, { "page": "make.continuing.params", "title": "Generates an R object containing the last parameter values of an MCMC run (to be used for a subsequent run)", "topics": [ "make.continuing.params" ] }, { "page": "MCMC", "title": "Runs the Markov chain Monte Carlo with the standard (Binomial) model", "topics": [ "MCMC" ] }, { "page": "MCMC_BB", "title": "Runs the Markov chain Monte Carlo with the overdispersion (Beta-Binomial) model", "topics": [ "MCMC_BB" ] }, { "page": "mcmc.operators", "title": "Operator parameters that control the operation of the MCMC", "topics": [ "mcmc.operators" ] }, { "page": "plot_acceptance_rate", "title": "Plots the acceptance rate of a parameter across MCMC generations", "topics": [ "plot_acceptance_rate" ] }, { "page": "plot_all_acceptance_rates", "title": "Plots the acceptance rates of all parameters across MCMC generations", "topics": [ "plot_all_acceptance_rates" ] }, { "page": "plot_all_joint_marginals", "title": "Plots the joint marginals for all parameter pairs", "topics": [ "plot_all_joint_marginals" ] }, { "page": "plot_all_marginals", "title": "Plots the marginal densities for all parameters", "topics": [ "plot_all_marginals" ] }, { "page": "plot_all_phi_marginals", "title": "Plot all the marginals for the phi parameters for all populations", "topics": [ "plot_all_phi_marginals" ] }, { "page": "plot_all_phi_trace", "title": "Plots all the trace plots for the phi parameters for all populations", "topics": [ "plot_all_phi_trace" ] }, { "page": "plot_all_trace", "title": "Plots all the trace plots for all parameters", "topics": [ "plot_all_trace" ] }, { "page": "plot_joint_marginal", "title": "Plots the joint marginal for a pair of parameters", "topics": [ "plot_joint_marginal" ] }, { "page": "plot_marginal", "title": "Plots the marginal density of a parameter", "topics": [ "plot_marginal" ] }, { "page": "plot_phi_marginal", "title": "Plots the marginal for the phi parameter estimated in a single population", "topics": [ "plot_phi_marginal" ] }, { "page": "plot_phi_trace", "title": "Plots the trace plot for the phi parameter estimated in a single population", "topics": [ "plot_phi_trace" ] }, { "page": "plot_posterior_predictive_samples", "title": "Plots posterior predictive sampling", "topics": [ "plot_posterior_predictive_samples" ] }, { "page": "plot_trace", "title": "Plot the trace plot for a parameter", "topics": [ "plot_trace" ] }, { "page": "posterior.predictive.sample", "title": "Generates posterior predictive samples", "topics": [ "posterior.predictive.sample" ] } ], "_rundeps": [ "bbmle", "bdsmatrix", "coda", "emdbook", "lattice", "MASS", "Matrix", "matrixcalc", "mvtnorm", "numDeriv", "plyr", "Rcpp" ], "_score": 3.255272505103306, "_indexed": true, "_nocasepkg": "bedassle", "_universes": [ "gbradburd" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.6.1", "date": "2026-10-05T08:27:13.000Z", "distro": "resolute", "commit": "72da7d622fb526ee5dae40a408f5ab66f470282e", "fileid": "https://r2.ropensci.org/8c820068455519015d3f667b8847d50142d7ffd6a7d3b593f1c74861d6df37a7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gbradburd/actions/runs/37283211148" }, { "r": "4.6.1", "os": "linux", "version": "1.6.1", "date": "2026-10-05T08:27:11.000Z", "distro": "resolute", "commit": "72da7d622fb526ee5dae40a408f5ab66f470282e", "fileid": "https://r2.ropensci.org/a4535f18566e8c31df035e55ac4f8034c698b4f020017ea6c472d2a591e605fd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gbradburd/actions/runs/37283211148" }, { "r": "4.5.3", "os": "mac", "version": "1.6.1", "date": "2026-10-05T08:27:46.000Z", "commit": "72da7d622fb526ee5dae40a408f5ab66f470282e", "fileid": "https://r2.ropensci.org/0b883e33a0f557d4dd644c8d4f911a68bb3cc6ba5ed47a7cc54bfa5cd235be2b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gbradburd/actions/runs/37283211148" }, { "r": "4.6.1", "os": "mac", "version": "1.6.1", "date": "2026-10-05T08:27:35.000Z", "commit": "72da7d622fb526ee5dae40a408f5ab66f470282e", "fileid": "https://r2.ropensci.org/af7ee18a40345d5c5b934c1ddae16ab595bcb25d6388972e4f301ab958230afc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gbradburd/actions/runs/37283211148" }, { "r": "4.6.0", "os": "wasm", "version": "1.6.1", "date": "2026-10-05T08:26:53.000Z", "commit": "72da7d622fb526ee5dae40a408f5ab66f470282e", "fileid": "https://r2.ropensci.org/a8cc9053400cd0010b45680dee4f3db8a4a60e121b24c5d363b618447717345b", "status": "success", "buildurl": "https://github.com/r-universe/gbradburd/actions/runs/37283211148" }, { "r": "4.7.0", "os": "win", "version": "1.6.1", "date": "2026-10-05T08:26:37.000Z", "commit": "72da7d622fb526ee5dae40a408f5ab66f470282e", "fileid": "https://r2.ropensci.org/ddee9f6d392585c4b5caed4d77b52e303cf364c82a910a3a8d0f5d0bd1302236", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gbradburd/actions/runs/37283211148" }, { "r": "4.5.3", "os": "win", "version": "1.6.1", "date": "2026-10-05T08:26:23.000Z", "commit": "72da7d622fb526ee5dae40a408f5ab66f470282e", "fileid": "https://r2.ropensci.org/abbe1a66ccb50779696b46fae9f8bc3833f709c96ef8db81aac5cc697d7ad571", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gbradburd/actions/runs/37283211148" }, { "r": "4.6.1", "os": "win", "version": "1.6.1", "date": "2026-10-05T08:26:24.000Z", "commit": "72da7d622fb526ee5dae40a408f5ab66f470282e", "fileid": "https://r2.ropensci.org/ed0345d9ba90f9679110c3d2b5ad00dadf0ac93bb9c2558059a819623dc548b5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gbradburd/actions/runs/37283211148" } ] }