Plotting is a bonus, not the core feature | Built-in plot functions | Sentinel test positivity | SARS-CoV-2 variants | ILI/ARI consultation rates | SARI rates | SARI virological data | Non-sentinel severity | Non-sentinel tests/detections | Quick plot shortcuts | Using the generic plot_erviss_data() | Customizing plots | Changing the theme | Modifying axes | Adding titles and annotations | Changing colours | Building your own plots from scratch

Introduction | Available data sources | Sentinel test positivity | SARS-CoV-2 variants | ILI/ARI consultation rates | SARI rates | SARI virological data | Non-sentinel severity | Non-sentinel tests and detections | Using the generic function | Historical snapshots | URL helpers | Using a local CSV file | Analyzing the data

Mathematical Formulas | 1. Number of events averted by vaccination (NAE) | 2. Number of avertable events considering an increase in final coverage (NAbE) | 3. Number Needed to Vaccinate (NNV) | Machado et al. method | Tuite and Fisman method | Example | NAE | NAbE | NNV | References

Description | Background | 1. Datasets to be used in the Epidemiological Report package | 1.1. Disease dataset specification | 1.2. Report parameters dataset specification | 1.3. Member States correspondence table dataset | 2. How to generate the Epidemiological Report in Microsoft Word format | 2.1. External disease dataset | 2.2. Word template | 2.3. Word bookmarks | 3. How to generate each epidemiological outputs independently | 3.1. Table: distribution of cases by Member State | 3.2. Seasonality plot: distribution of cases by month | 3.3. Trend plot: trend and number of cases by month | 3.4. Maps: distribution of cases by Member State | 3.5. Age and gender bar graph