EpiNow2
| REF | Wellcome report |
| Docs | Docs |
| Github | Github |
| Last commit | Feb 25, 2021 |
| Installation | Installation |
Brief Description
EpiNow2 estimates the time-varying reproduction number on cases by date of infection (using a similar approach to that implemented in EpiEstim). True infections, treated as latent and unobserved, are estimated and then mapped to observed data (for example cases by date of report) via one or more delay distributions (in the examples in the package documentation these are an incubation period and a reporting delay) and a reporting model that can include weekly periodicity.
Uncertainty is propagated from all inputs into the final parameter estimates, helping to mitigate spurious findings. This is handled internally. The time-varying reproduction estimates and the uncertain generation time also give time-varying estimates of the rate of growth.
Forecasting is also supported for the time-varying reproduction number, infections, and reported cases using the same generative process approach as used for estimation.
Important links:
Methods
This package contains the following methods:
Assessment
| Features | |
| Ability to nowcast/forecast | Yes |
| Incorporates delay distributions | Yes |
| Estimates expected cases | Yes |
| Communicates uncertainty | Yes |
| Validation | |
| Documentation of package methods | Yes |
| Documentation of package implementation | Yes |