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  "Title": "Quantifies Effects of Geo/Eco Distance on Genetic\nDifferentiation",
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  "Date": "2024-1-09",
  "Author": "Gideon Bradburd",
  "Maintainer": "Gideon Bradburd <bradburd@umich.edu>",
  "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",
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    "User": "root"
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  "Date/Publication": "2024-01-12 02:39:37 UTC",
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    {
      "package": "matrixcalc",
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    {
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    "extra/citation.html",
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    "extra/contents.json",
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  "_cranurl": false,
  "_releases": [
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      "date": "2013-07-31"
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    },
    {
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      "date": "2013-10-01"
    },
    {
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      "date": "2014-01-25"
    },
    {
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      "date": "2014-06-10"
    },
    {
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      "date": "2014-12-03"
    },
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      "date": "2022-04-10"
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    "BB_Update_mu",
    "BB_Update_phi",
    "BB_Update_thetas",
    "calculate.all.pairwise.Fst",
    "calculate.pairwise.Fst",
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    "identify_invariant_loci",
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    "Likelihood_counts",
    "Likelihood_thetas",
    "link.up.posteriors",
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    "load_posterior_predictive_samples",
    "make.continuing.params",
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    "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"
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      "file": "mcmc.operators.rda",
      "class": [
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      ],
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    }
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    {
      "page": "BEDASSLE-package",
      "title": "Disentangling the contributions of geographic and ecological isolation to genetic differentiation",
      "topics": [
        "BEDASSLE-package",
        "BEDASSLE"
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    {
      "page": "BEDASSLE-internal",
      "title": "Internal BEDASSLE Functions",
      "topics": [
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        "BB_Likelihood_counts",
        "BB_Prior_prob_phi",
        "BB_Update_mu",
        "BB_Update_phi",
        "BB_Update_thetas",
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        "Likelihood_counts",
        "Likelihood_thetas",
        "load_MCMC_output",
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        "Update_beta",
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      ]
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      ]
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      "title": "Runs the Markov chain Monte Carlo with the standard (Binomial) model",
      "topics": [
        "MCMC"
      ]
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      ]
    },
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      "topics": [
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      "topics": [
        "plot_acceptance_rate"
      ]
    },
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      "page": "plot_all_acceptance_rates",
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      "topics": [
        "plot_all_acceptance_rates"
      ]
    },
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      "topics": [
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      ]
    },
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      "title": "Plots the marginal densities for all parameters",
      "topics": [
        "plot_all_marginals"
      ]
    },
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      "topics": [
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      ]
    },
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    },
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