The two things you provide | Configuration lives outside the repository | Accounts | Closing the app to anonymous visitors | Watching sign-ins | Where the database lives | Which servers this is tested against | Sharing a schema with something else | If you already have a MariaDB or MySQL database | Upgrading EpiSODIC | What a migration does, and does not do | When the schema is not the application's to change | Going back | Running the app | Behind a reverse proxy | Custom report templates | Scheduled reports | Optional pieces, and their fallbacks | Notifications | See also

Checking what they actually delivered

What a plugin can do | Using plugins | Installing and switching on | What you see | Pushing a plugin's button | Keeping it safe | Working from a script | Developing a plugin | Every key | Steps | Placeholders | What a step receives | The payload | Reporting back | When something goes wrong | Limitations | Versions | See also

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 | Export | Plugins | Access | Database | Per-pathogen CSV columns | See also

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) | See also

Setting up: identity and keys | Exporting | What leaves the instance | Importing | Geography the receiver cannot place | Scheduling: the Import and export screen | Transport | What importing and exporting do not solve | Data protection | File format | See also

The lattice: streams, not one big feed | Four detectors, not one algorithm | Scale routing: outbreaks and epidemics | Reconciliation: turning detections into outbreaks and epidemics | Epidemic closure | The "during" link | Suppression: one lattice, not five parallel views | Derived state, not a stored status | Declarations: a human act

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

Getting your data in | Running it day to day | Accounts and hosting

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 | See also

Setting up a schedule | Cadence and delivery | What changed since last time | The email itself | Custom report templates and patient-level detail | See also

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

Introduction | The Plot2 Philosophy: Less Typing, More Plotting | Getting Started with plot2() | Basic Usage: Let plot2() Do the Work | Customising the Plot Type | A Closer Look at the Axes | Setting Up Basic Axes | Working with Multiple Variables | Delving into Categories | Basic Grouping | Customising Categories | Exploring Facets | Basic Faceting | Advanced Faceting Options | Leveraging In-line Transformations with plot2() | Aggregations Made Easy | Combining Data with In-line Transformations | In-line Math Transformations | Advanced Formatting on the Fly | Combining Everything Together | Sorting and Limiting Data | Basic Sorting | Sorting Alphabetically | Sorting with a Custom Order | Limiting Data | Combining Sorting with Limiting | Visualising Sorting Options | Customising Colours | Using Pre-set Colour Scales | Defining Custom Colours | Default Colours | Advanced Plot Types | Adding Elements with add_*() Functions | Adding Lines, Points, and Columns | Adding Points | Adding Columns | Plotting Error Bars | Adding Spatial Features with add_sf() | Customising Fonts in plot2() | Using System Fonts and Google Fonts | Creating Consistent Themes with Fonts | Discussion | Enhancing Workflow Efficiency | A Natural Extension of ggplot2 | Flexibility Without Complexity | Philosophical Underpinnings | Reflecting on Usage Scenarios | Looking Forward

Column / Bar | Line | Point | Area | Boxplot / Violin | Histogram | Geo (sf) | Beeswarm | Back-to-back | Sankey | Spider | UpSet | Dumbbell

Initialisation | Title Page | title | subtitle / subtitle2 | author | date | identifier | titlepage-logo | Alignment | Figures, Tables, and Table of Contents | Colours | Using colour-main | Colour of Callout Blocks | Fonts | Footer | Examples | Example 1: Default | Example 2: Colour change | Example 3: Full page colour