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  "Title": "Strain Level Microbiome Wide Association Studies",
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  "Description": "Fits statistical models to detect microbial strains\nassociated with a phenotype. For small sample sizes, models can\nbe fitted using empirical Bayes maximum a posteriori (MAP)\npriors to improve detection power. Supports various\nexperimental design scenarios, including repeated measures.",
  "License": "MIT + file LICENSE",
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    "abundanceFit",
    "ani_distance",
    "caseControlFit",
    "comp_ani_diff_and_posthoc_test",
    "compute_eb_priors",
    "define_priors",
    "estimate_beta_diversity",
    "estimate_sample_richness",
    "extract_fixef_priors",
    "extract_strainspy",
    "filter_by_presence",
    "getContigNames",
    "getFDR",
    "getGenomes",
    "getResiduals",
    "getSamples",
    "getZICoefficients",
    "glmObFit",
    "glmQBFit",
    "glmZiBFit",
    "hadjust",
    "merge_metaphlan_files",
    "merge_sourmash_files",
    "merge_sylph_files",
    "modify_metadata",
    "plot_ani_dist",
    "plot_histogram",
    "plot_manhattan",
    "plot_mds",
    "plot_pca_biplot",
    "plot_prior_bootstrap",
    "plot_volcano",
    "prep_for_prediction",
    "read_metaphlan",
    "read_sourmash",
    "read_sylph",
    "read_taxonomy",
    "show",
    "strainspy",
    "summary",
    "top_hits"
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    {
      "page": "abundanceFit",
      "title": "abundanceFit",
      "topics": [
        "abundanceFit"
      ]
    },
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      "page": "ani_distance",
      "title": "ani_distance",
      "topics": [
        "ani_distance"
      ]
    },
    {
      "page": "caseControlFit",
      "title": "caseControlFit",
      "topics": [
        "caseControlFit"
      ]
    },
    {
      "page": "check_progress",
      "title": "Validate a 'progress' argument",
      "topics": [
        "check_progress"
      ]
    },
    {
      "page": "check_unique_names",
      "title": "Stop if sample or feature names are not unique",
      "topics": [
        "check_unique_names"
      ]
    },
    {
      "page": "clean_contig_names",
      "title": "Automatically clean contig names for plots",
      "topics": [
        "clean_contig_names"
      ]
    },
    {
      "page": "comp_ani_diff_and_posthoc_test",
      "title": "Compute the mean ANI differences for contigs with an identity effect and perform posthoc testing to establish support for each hit.",
      "topics": [
        "comp_ani_diff_and_posthoc_test"
      ]
    },
    {
      "page": "compute_eb_priors",
      "title": "Constructor for strainspy_priors using empirical Bayes estimation",
      "topics": [
        "compute_eb_priors"
      ]
    },
    {
      "page": "define_priors",
      "title": "Constructor for strainspy_priors using preset or user defined priors",
      "topics": [
        "define_priors"
      ]
    },
    {
      "page": "estimate_beta_diversity",
      "title": "Estimate beta diversity from ANI",
      "topics": [
        "estimate_beta_diversity"
      ]
    },
    {
      "page": "estimate_sample_richness",
      "title": "Estimate species richness and coverage of reference strains using ANI",
      "topics": [
        "estimate_sample_richness"
      ]
    },
    {
      "page": "extract_fixef_priors",
      "title": "Access fixef priors needed for ordinal beta regression",
      "topics": [
        "extract_fixef_priors",
        "extract_fixef_priors,strainspy_priors-method"
      ]
    },
    {
      "page": "extract_strainspy",
      "title": "Extract data from a StrainSpy 'SummarizedExperiment' object in long format",
      "topics": [
        "extract_strainspy"
      ]
    },
    {
      "page": "failed_fit_index",
      "title": "Identify per-feature model fits that failed",
      "topics": [
        "failed_fit_index"
      ]
    },
    {
      "page": "filter_by_presence",
      "title": "filter_by_presence",
      "topics": [
        "filter_by_presence"
      ]
    },
    {
      "page": "filter_by_presence_and_rescale",
      "title": "filter_by_presence_with_rescale_abundance",
      "topics": [
        "filter_by_presence_and_rescale"
      ]
    },
    {
      "page": "filter_by_presence_longitudinal",
      "title": "Filter strains based on subject and time aware manner - useful for longitudinal datasets",
      "topics": [
        "filter_by_presence_longitudinal"
      ]
    },
    {
      "page": "fit_lm",
      "title": "Fit a linear model for a Single Feature",
      "topics": [
        "fit_lm"
      ]
    },
    {
      "page": "fit_lmer",
      "title": "Fit a linear model with random effects for a single feature",
      "topics": [
        "fit_lmer"
      ]
    },
    {
      "page": "fit_logit_model",
      "title": "Fit Logistic Regression for a Single Feature",
      "topics": [
        "fit_logit_model"
      ]
    },
    {
      "page": "fit_ob_model",
      "title": "Fit Ordinal Beta Regression for a Single Feature",
      "topics": [
        "fit_ob_model"
      ]
    },
    {
      "page": "fit_qb_model",
      "title": "Fit quasibinomial regression for a Single Feature",
      "topics": [
        "fit_qb_model"
      ]
    },
    {
      "page": "fit_zero_inflated_beta",
      "title": "Fit Zero-Inflated Beta Regression for a Single Feature",
      "topics": [
        "fit_zero_inflated_beta"
      ]
    },
    {
      "page": "fit_zero_inflated_beta_gamlss",
      "title": "Fit Zero-Inflated Beta Regression for a Single Feature using the gamlss package",
      "topics": [
        "fit_zero_inflated_beta_gamlss"
      ]
    },
    {
      "page": "get_colors",
      "title": "Generate colours for Manhattan plots",
      "topics": [
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      ]
    },
    {
      "page": "get_confusion_mx",
      "title": "Generate a confusion matrix for a fitted model",
      "topics": [
        "get_confusion_mx"
      ]
    },
    {
      "page": "getContigNames",
      "title": "Get Contig names in a fit object",
      "topics": [
        "getContigNames",
        "getContigNames,strainspy_fit-method"
      ]
    },
    {
      "page": "getFDR",
      "title": "Access False Discovery Rates (FDR)",
      "topics": [
        "getFDR",
        "getFDR,strainspy_fit-method"
      ]
    },
    {
      "page": "getGenomes",
      "title": "Get Genomes in a fit object",
      "topics": [
        "getGenomes",
        "getGenomes,strainspy_fit-method"
      ]
    },
    {
      "page": "getResiduals",
      "title": "Access Residuals",
      "topics": [
        "getResiduals",
        "getResiduals,strainspy_fit-method"
      ]
    },
    {
      "page": "getSamples",
      "title": "Get Sample names in a fit object",
      "topics": [
        "getSamples",
        "getSamples,strainspy_fit-method"
      ]
    },
    {
      "page": "getZICoefficients",
      "title": "Access Zero-Inflation Coefficients",
      "topics": [
        "getZICoefficients",
        "getZICoefficients,strainspy_fit-method"
      ]
    },
    {
      "page": "glmObFit",
      "title": "glmObFit",
      "topics": [
        "glmObFit"
      ]
    },
    {
      "page": "glmQBFit",
      "title": "glmQBFit TODO: Implement return of vcov info. Patched for compatibility (returns NULL)",
      "topics": [
        "glmQBFit"
      ]
    },
    {
      "page": "glmZiBFit",
      "title": "glmZiBFit",
      "topics": [
        "glmZiBFit"
      ]
    },
    {
      "page": "hadjust",
      "title": "Performs hierarchical taxonomy aware adjustment of p-values.",
      "topics": [
        "hadjust"
      ]
    },
    {
      "page": "merge_metaphlan_files",
      "title": "merge_metaphlan_files",
      "topics": [
        "merge_metaphlan_files"
      ]
    },
    {
      "page": "merge_sourmash_files",
      "title": "merge_sourmash_files",
      "topics": [
        "merge_sourmash_files"
      ]
    },
    {
      "page": "merge_sylph_files",
      "title": "merge_sylph_files",
      "topics": [
        "merge_sylph_files"
      ]
    },
    {
      "page": "modify_metadata",
      "title": "Add or modify metadata in a 'SummarizedExperiment' object",
      "topics": [
        "modify_metadata"
      ]
    },
    {
      "page": "nobars_",
      "title": "Remove random effects from model",
      "topics": [
        "nobars_"
      ]
    },
    {
      "page": "offset_ANI",
      "title": "Offset ANI by a fixed value",
      "topics": [
        "offset_ANI"
      ]
    },
    {
      "page": "plot_ani_dist",
      "title": "Generate a violin or box plot for a subset of contigs for a categorical phenotype.",
      "topics": [
        "plot_ani_dist"
      ]
    },
    {
      "page": "plot_histogram",
      "title": "Generate a histogram for a single contig for a categorical phenotype.",
      "topics": [
        "plot_histogram"
      ]
    },
    {
      "page": "plot_manhattan",
      "title": "Generate a strain Manhattan plot from a strainspy_fit object",
      "topics": [
        "plot_manhattan"
      ]
    },
    {
      "page": "plot_manhattan_gt",
      "title": "Generate a Manhattan plot from a strainspy_fit object, with the option to add ground truth",
      "topics": [
        "plot_manhattan_gt"
      ]
    },
    {
      "page": "plot_manhattan_tree",
      "title": "Generate a 'conventional' Manhattan plot for the strain all strains.",
      "topics": [
        "plot_manhattan_tree"
      ]
    },
    {
      "page": "plot_mds",
      "title": "Plot MDS of ANI data",
      "topics": [
        "plot_mds"
      ]
    },
    {
      "page": "plot_pca_biplot",
      "title": "plot_pca_biplot",
      "topics": [
        "plot_pca_biplot"
      ]
    },
    {
      "page": "plot_prior_bootstrap",
      "title": "Plot method for strainspy_priors objects",
      "topics": [
        "plot_prior_bootstrap",
        "plot_prior_bootstrap,strainspy_priors-method"
      ]
    },
    {
      "page": "plot_volcano",
      "title": "Generate a Volcano Plot from a betaGLM Object",
      "topics": [
        "plot_volcano"
      ]
    },
    {
      "page": "prep_for_prediction",
      "title": "Prepare a caret-compatible prediction data frame from a SummarizedExperiment",
      "topics": [
        "prep_for_prediction"
      ]
    },
    {
      "page": "read_metaphlan",
      "title": "read_metaphlan",
      "topics": [
        "read_metaphlan"
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    },
    {
      "page": "read_sourmash",
      "title": "read_sourmash",
      "topics": [
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      ]
    },
    {
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