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  "Title": "Joint estimation of COI and population structure for malaria\ngenetic data",
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  "Maintainer": "Bob Verity <r.verity@imperial.ac.uk>",
  "Description": "Carries out joint estimation of complexity of infection\n(COI) and population structure on malaria genetic data. Assumes\na simple model in which individuals have genotypes sampled from\none or more subpopulations, and the number of genotypes in an\nindividual is equal to the COI, which is also unknown. All\nunknown parameters are inferred using MCMC.",
  "License": "MIT + file LICENSE",
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  "Repository": "https://plasmogenepi.r-universe.dev",
  "Date/Publication": "2019-02-26 14:55:58 UTC",
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    "description": "We are a network of scientists who have come together since 2018 to address challenges in malaria genomic epidemiology."
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    "bind_data_biallelic",
    "bind_data_multiallelic",
    "check_MALECOT_loaded",
    "delete_set",
    "get_ESS",
    "get_group_order",
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    "malecot_file",
    "malecot_project",
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    "plot_COI",
    "plot_COI_mean",
    "plot_coupling",
    "plot_density",
    "plot_e",
    "plot_GTI_path",
    "plot_logevidence_K",
    "plot_logevidence_model",
    "plot_loglike",
    "plot_loglike_dignostic",
    "plot_p",
    "plot_posterior_K",
    "plot_posterior_model",
    "plot_prior_COI",
    "plot_prior_p",
    "plot_structure",
    "plot_trace",
    "print_full",
    "recalculate_evidence",
    "run_mcmc",
    "sim_data",
    "sim_data_safe"
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    {
      "page": "active_set",
      "title": "Change the active set of a MALECOT project",
      "topics": [
        "active_set"
      ]
    },
    {
      "page": "bind_data_biallelic",
      "title": "Bind bi-allelic data to project",
      "topics": [
        "bind_data_biallelic"
      ]
    },
    {
      "page": "bind_data_multiallelic",
      "title": "Bind multi-allelic format data to project",
      "topics": [
        "bind_data_multiallelic"
      ]
    },
    {
      "page": "check_MALECOT_loaded",
      "title": "Check that MALECOT package has loaded successfully",
      "topics": [
        "check_MALECOT_loaded"
      ]
    },
    {
      "page": "delete_set",
      "title": "Delete parameter set",
      "topics": [
        "delete_set"
      ]
    },
    {
      "page": "get_ESS",
      "title": "Get ESS",
      "topics": [
        "get_ESS"
      ]
    },
    {
      "page": "get_group_order",
      "title": "Match grouping against q-matrix",
      "topics": [
        "get_group_order"
      ]
    },
    {
      "page": "is.malecot_project",
      "title": "Determine if object is of class malecot_project",
      "topics": [
        "is.malecot_project"
      ]
    },
    {
      "page": "MALECOT",
      "title": "MALECOT package",
      "topics": [
        "MALECOT-package",
        "MALECOT"
      ]
    },
    {
      "page": "malecot_file",
      "title": "Import file",
      "topics": [
        "malecot_file"
      ]
    },
    {
      "page": "malecot_project",
      "title": "Define empty malecot_project object",
      "topics": [
        "malecot_project"
      ]
    },
    {
      "page": "more_colours",
      "title": "Expand series of colours by interpolation",
      "topics": [
        "more_colours"
      ]
    },
    {
      "page": "new_set",
      "title": "Create new MALECOT parameter set",
      "topics": [
        "new_set"
      ]
    },
    {
      "page": "plot_acf",
      "title": "Produce MCMC autocorrelation plot",
      "topics": [
        "plot_acf"
      ]
    },
    {
      "page": "plot_COI",
      "title": "Plot COI 95% credible intervals",
      "topics": [
        "plot_COI"
      ]
    },
    {
      "page": "plot_COI_mean",
      "title": "Plot COI_mean 95% credible intervals",
      "topics": [
        "plot_COI_mean"
      ]
    },
    {
      "page": "plot_coupling",
      "title": "Plot Metropolis-coupling acceptance rates",
      "topics": [
        "plot_coupling"
      ]
    },
    {
      "page": "plot_density",
      "title": "Produce MCMC density plot",
      "topics": [
        "plot_density"
      ]
    },
    {
      "page": "plot_e",
      "title": "Plot error rate 95% credible intervals",
      "topics": [
        "plot_e"
      ]
    },
    {
      "page": "plot_GTI_path",
      "title": "Plot GTI path of current active set",
      "topics": [
        "plot_GTI_path"
      ]
    },
    {
      "page": "plot_logevidence_K",
      "title": "Plot log-evidence estimates over K",
      "topics": [
        "plot_logevidence_K"
      ]
    },
    {
      "page": "plot_logevidence_model",
      "title": "Plot log-evidence estimates over parameter sets",
      "topics": [
        "plot_logevidence_model"
      ]
    },
    {
      "page": "plot_loglike",
      "title": "Plot loglikelihood 95% credible intervals",
      "topics": [
        "plot_loglike"
      ]
    },
    {
      "page": "plot_loglike_dignostic",
      "title": "Produce diagnostic plots of log-likelihood",
      "topics": [
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      ]
    },
    {
      "page": "plot_p",
      "title": "Plot allele frequency 95% credible intervals",
      "topics": [
        "plot_p"
      ]
    },
    {
      "page": "plot_posterior_K",
      "title": "Plot posterior K",
      "topics": [
        "plot_posterior_K"
      ]
    },
    {
      "page": "plot_posterior_model",
      "title": "Plot posterior model",
      "topics": [
        "plot_posterior_model"
      ]
    },
    {
      "page": "plot_prior_COI",
      "title": "Plot prior on COI",
      "topics": [
        "plot_prior_COI"
      ]
    },
    {
      "page": "plot_prior_p",
      "title": "Plot prior on allele frequencies",
      "topics": [
        "plot_prior_p"
      ]
    },
    {
      "page": "plot_structure",
      "title": "Posterior allocation plot",
      "topics": [
        "plot_structure"
      ]
    },
    {
      "page": "plot_trace",
      "title": "Produce MCMC trace plot",
      "topics": [
        "plot_trace"
      ]
    },
    {
      "page": "print_full",
      "title": "Ordinary print function for class malecot_project",
      "topics": [
        "print_full"
      ]
    },
    {
      "page": "print.malecot_project",
      "title": "Custom print function for class malecot_project",
      "topics": [
        "print.malecot_project"
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    },
    {
      "page": "recalculate_evidence",
      "title": "Recalculate evidence and posterior estimates",
      "topics": [
        "recalculate_evidence"
      ]
    },
    {
      "page": "run_mcmc",
      "title": "Run main MCMC",
      "topics": [
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      ]
    },
    {
      "page": "sim_data",
      "title": "Simulate genetic data",
      "topics": [
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    },
    {
      "page": "sim_data_safe",
      "title": "Simulate genetic data subject to constraints",
      "topics": [
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      ]
    },
    {
      "page": "summary.malecot_project",
      "title": "Print summary for class malecot_project",
      "topics": [
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      ]
    }
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        "Plot results",
        "Structure plots",
        "Posterior COI plots",
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      "headings": [
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      "modified": "2018-10-01 16:39:19",
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        "page 2"
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        "Installing and loading MALECOT"
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      "author": "Bob Verity",
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        "More realistic priors on COI",
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        "Missing data and errors"
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        "Structure plots",
        "Posterior COI plots",
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        "More realistic priors on allele frequencies"
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      "created": "2018-09-25 06:39:44",
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