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    "episodic_mail_template_preview",
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    "episodic_ui_trend_chart",
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      ]
    },
    {
      "page": "episodic_add_user",
      "title": "Create an Account for a New Epidemiologist or Viewer",
      "topics": [
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    {
      "page": "episodic_auth",
      "title": "How sign-in works",
      "topics": [
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      ]
    },
    {
      "page": "episodic_case_data",
      "title": "Connect your own laboratory data",
      "topics": [
        "episodic_case_data"
      ]
    },
    {
      "page": "episodic_charts",
      "title": "Draw the Dashboard Charts (Epidemic Curve, Trend, and Rt)",
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        "episodic_ui_epi_curve_chart",
        "episodic_ui_rt_chart",
        "episodic_ui_trend_chart"
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    },
    {
      "page": "episodic_check_cases",
      "title": "Check Your Case Data Before You Hand It to EpiSODIC",
      "topics": [
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      ]
    },
    {
      "page": "episodic_check_denominators",
      "title": "Check Your Positivity Data Before You Hand It to EpiSODIC",
      "topics": [
        "episodic_check_denominators"
      ]
    },
    {
      "page": "episodic_check_institution_activity",
      "title": "Check Your Hospital Activity Data Before You Hand It to EpiSODIC",
      "topics": [
        "episodic_check_institution_activity"
      ]
    },
    {
      "page": "episodic_config_export",
      "title": "Export the Resolved Configuration as a Zip File",
      "topics": [
        "episodic_config_export"
      ]
    },
    {
      "page": "episodic_db_connect",
      "title": "Connect to an Existing EpiSODIC Database",
      "topics": [
        "episodic_db_connect"
      ]
    },
    {
      "page": "episodic_db_create",
      "title": "Set Up a New EpiSODIC Database",
      "topics": [
        "episodic_db_create"
      ]
    },
    {
      "page": "episodic_db_dsn_mariadb",
      "title": "Connect EpiSODIC to a MariaDB or MySQL Server",
      "topics": [
        "episodic_db_dsn_mariadb",
        "episodic_db_dsn_mysql"
      ]
    },
    {
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      "topics": [
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      "title": "Connect Using the 'EPISODIC_DB' Environment Variable",
      "topics": [
        "episodic_db_open"
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    {
      "page": "episodic_db_truncate",
      "title": "Empty Every EpiSODIC Table, Keeping the Schema Itself",
      "topics": [
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    {
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      "title": "Try EpiSODIC With Synthetic Outbreak Data",
      "topics": [
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      "title": "Show Clusters on a Map",
      "topics": [
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        "episodic_geo_overlay_resolve",
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      "topics": [
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    {
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      "title": "How notifications work",
      "topics": [
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    {
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      "title": "Send a Test Notification Through All Configured Channels",
      "topics": [
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    {
      "page": "episodic_validate_comparator",
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      "title": "Measure Detection Against Known Truth",
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        "print.episodic_validation"
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      "page": "episodic_validate_rethreshold",
      "title": "Re-Match a Validation Result at Different Thresholds",
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      "title": "Getting your data in",
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      "headings": [
        "Cases (mandatory)",
        "source_key: one identifier per result, not per specimen",
        "One culture, more than one reported result",
        "Deduplication is EpiSODIC's job, not yours",
        "Check your data first",
        "Positivity metadata (optional)",
        "Institution activity (optional)",
        "Geographic reference data (optional)",
        "The choropleth map",
        "L4 (province-level) detection",
        "What a run reports",
        "Clusters from another system (optional)",
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      "title": "Measuring detection against known truth",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What it does",
        "The ground truth is data",
        "The two matching rules",
        "What it reports, and how to read it",
        "A comparator, and a control",
        "Which detector earns its place",
        "Where the real numbers live"
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      "engine": "knitr::rmarkdown",
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        "Where to configure",
        "Minimal example: ntfy",
        "ntfy with authentication",
        "SMTP (Gmail, institutional relay, any SMTP server)",
        "sendmail (Linux/Unix)",
        "Microsoft 365",
        "Option A: App-only (client credentials) -- recommended for unattended cron",
        "Option B: Delegated (cached interactive token)",
        "Option C: Reuse an already-cached login (no app registration needed)",
        "Microsoft Teams",
        "Setting up the webhook",
        "Slack",
        "Triggers",
        "Dashboard link",
        "Full reference example",
        "Testing your setup",
        "What a notification looks like",
        "New clusters",
        "Run failure",
        "Colours and font",
        "Your own email layout",
        "Troubleshooting",
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        "No dependency on any one laboratory system",
        "Three altitudes",
        "The Outbreaks screen: one outbreak at a time",
        "The Epidemics screen: regional and seasonal",
        "The Pathogen screen: one pathogen over a period",
        "Beyond the three altitudes",
        "The Performance screen: is detection itself working",
        "The Archive screen: last winter's precedent",
        "Streams and Activity: how the machinery is behaving",
        "The Info screen",
        "The Settings screen",
        "Where to go next"
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      "engine": "knitr::rmarkdown",
      "headings": [
        "Setting up a schedule",
        "Cadence and delivery",
        "What changed since last time",
        "The email itself",
        "Custom report templates and patient-level detail",
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      "created": "2026-09-06 11:48:08",
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      "source": "tuning-detection.Rmd",
      "filename": "tuning-detection.html",
      "title": "Tuning detection for your catchment",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Before you change anything",
        "Too many false alarms",
        "The Farrington bound is too narrow",
        "same_place fires on endemic patterns",
        "Suppression lets redundant signals through",
        "Missing outbreaks",
        "Farrington never fits",
        "same_place thresholds are too high",
        "The eligibility gate excludes a stream",
        "Clusters close too early or too late",
        "Clusters close before the outbreak is really over",
        "Clusters stay open long after the last case",
        "Cooldown absorption swallows a real recurrence",
        "Priority ranking does not match your triage",
        "Seasonal detection is wrong",
        "MEM never runs",
        "MEM fires too early or too late",
        "Per-pathogen parameters",
        "Verifying that a change helped",
        "Against synthetic ground truth",
        "Against your own board's verdicts",
        "Reference",
        "Reconciliation",
        "Eligibility",
        "Effect-size floor",
        "same_place detector",
        "Farrington detector",
        "MEM detector",
        "rare_trigger detector",
        "Nowcast",
        "Outbreak-end probability",
        "Epidemic direction",
        "Epidemic outlook",
        "Typical past season",
        "Priority score",
        "Scale",
        "Geography",
        "Suppression",
        "Notifications",
        "Report",
        "Access",
        "Database",
        "Per-pathogen CSV columns",
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      "created": "2026-09-19 15:17:09",
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