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

What does it do? | Fitting a gamma distribution to delay data | Converting a growth rate (r) to a reproduction number (R0) | Standardising labels | Anonymising data

Description | Example

Introduction | Converting dates to weeks | How does it work? | The aweek class | Best practices | Weekly aggregation | Factors | Weeks to weeks | Combining aweek objects | Dates can be appended to aweek objects | Add characters with caution | Working with weeks in data frames | weeks as numbers | weeks as characters | Converting weeks to dates

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

Installing the package | What does it do? | Estimation of risk | Example | Data structure to store flows and metadata | Basic methods | Plotting | Accessors | References

Introduction | Construction of the epiflows object from data frames | Using set_vars() to update variable keys in the object | Example: different durations of stay | data preparation | Using set_vars() | Using a custom argument | References

make_epicontacts() | $linelist | $contacts | Generics | print.epicontacts() | summary.epicontacts() | subset.epicontacts() | plot.epicontacts()

Why? | How it works | Mapping continuous values to an underlying discrete grid | Cumulative density function | Probability density function to probability mass function

Introduction | Loading Data | Example Dataset | Creating epicontacts Object | Data Manipulation | Access Unique Identifiers | Subsetting | Visualisation | Default Plotting Method | 3D plots | Analysis | Extract Characteristics of Pairwise Nodes | Identify Clusters | Calculate Degree | References