Background | A motivating example | The configuration file | The R directory | Putting it together | Changing things | Loading objects from the cache

Background | Scope | A motivating example | The configuration file | The R directory | Putting it together | Changing things | Multiple scenarios

What does it do? | Functions at a glance | Basic Usage | Computing incidence from a linelist | Computing incidence from pre-aggregated data | Plotting in style of European Programme for Intervention Epidemiology Training (EPIET) | Support for tidy-select semantics | Working with incidence objects | regroup() | complete_dates() | keep_first(), keep_last() and keep_peaks() | Bootstrapping and estimating peaks | cumulate() | Building on incidence2 | Class preservation | Accessing variable information | Grouping aware methods | Example fitting a poisson model | Example - Adding a rolling average

Introduction | Week groupings | Period grouping | yearmonth, yearquarter and year | month | Methods and other functionality | Acknowledgements

Example | Configuration file | Loading | Loading things as they are | Using other functions | Related work

Overview | The EQ5D object class | Usage | Coercion | Descriptive methods | Calculating utility values | QALY calculations | Other functionality | Paretian Classification of Health Change (PCHC)

Example data: simulated Ebola outbreak | The plot.incidence function | Default behaviour | Changing colors | The default palette | Using different palettes | Specifying colors manually | Example 1: changing a single color | Example 2: changing several colors (note that naming colors is optional) | Example 3: using color to highlight specific groups | Useful ggplot2 tweaks | Changing dates on the x-axis | Changing date format | Changing the grid | Handling non-ISO weeks | Labelling every bin | Changing the legend | Applying the style of European Programme for Intervention Epidemiology Training (EPIET) | Display individual cases

Installing the package | What does it do? | Worked example: simulated Ebola outbreak | Loading the data | Computing and plotting incidence | Handling incidence objects | Modelling incidence

Exporting results | Importing pre-computed incidence

Structure of an incidence object. | $dates | $counts | $timespan | $interval | $n | $weeks

Structure of an incidence_fit object | Building an incidence_fit object from scratch | Step 1: create the model | Step 2: creation of the $info list: | Step 3: combine lists and create object | Structure of an incidence_fit_list object | Example: A tale of two fits | Example: Nested incidence_fit