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    "show",
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      "title": "Compute the mean ANI differences for contigs with an identity effect and perform posthoc testing to establish support for each hit.",
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    },
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    {
      "page": "define_priors",
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      "title": "Estimate beta diversity from ANI",
      "topics": [
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    },
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      "title": "Estimate species richness and coverage of reference strains using ANI",
      "topics": [
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    },
    {
      "page": "extract_fixef_priors",
      "title": "Access fixef priors needed for ordinal beta regression",
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      "title": "Extract data from a StrainSpy 'SummarizedExperiment' object in long format",
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    {
      "page": "getContigNames",
      "title": "Get Contig names in a fit object",
      "topics": [
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        "getContigNames,strainspy_fit-method"
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    },
    {
      "page": "getGenomes",
      "title": "Get Genomes in a fit object",
      "topics": [
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        "getGenomes,strainspy_fit-method"
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      "title": "Access the prior specification table",
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    },
    {
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      "title": "Access Residuals",
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        "getResiduals,strainspy_fit-method"
      ]
    },
    {
      "page": "getSamples",
      "title": "Get Sample names in a fit object",
      "topics": [
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        "getSamples,strainspy_fit-method"
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    },
    {
      "page": "getZICoefficients",
      "title": "Access Zero-Inflation Coefficients",
      "topics": [
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      "page": "hadjust",
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      "topics": [
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    },
    {
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    {
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      "title": "Generate a strain Manhattan plot from a strainspy_fit object",
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    {
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      "title": "Plot MDS of ANI data",
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    {
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      "title": "Prepare a caret-compatible prediction data frame from a SummarizedExperiment",
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      "topics": [
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      "title": "Read and process a taxonomy file",
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      "title": "Show Method for strainspy_fit",
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        "getConvergence",
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        "getDesign",
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      "title": "Summary Method for strainspy_fit",
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      "title": "Provides the top results of a strainspy_fit object, sorted by adjusted p-value.",
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