EpiNow2
Estimate and Forecast Real-Time Infection Dynamics
Description
Estimates the time-varying reproduction number, rate of spread, and doubling time using a renewal equation approach combined with Bayesian inference via Stan. Supports Gaussian process and random walk priors for modelling changes in transmission over time. Accounts for delays between infection and observation (incubation period, reporting delays), right-truncation in recent data, day-of-week effects, and observation overdispersion. Can estimate relationships between primary and secondary outcomes (e.g., cases to hospitalisations or deaths) and forecast both. Runs across multiple regions in parallel. Based on Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1> and Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>.
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CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 25, 2026
NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 22, 2026
package dependencies
Package suggested but not available for checking: ‘cmdstanr’
package dependencies
Package suggested but not available for checking: ‘cmdstanr’
package dependencies
Package suggested but not available for checking: 'cmdstanr'
ERROR 10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 18, 2026
whether package can be installed
Installation failed. See 'd:/Rcompile/CRANpkg/local/4.6/EpiNow2.Rcheck/00install.out' for details.
package dependencies
Package suggested but not available for checking: ‘cmdstanr’
package dependencies
Package suggested but not available for checking: ‘cmdstanr’
package dependencies
Package suggested but not available for checking: 'cmdstanr'
NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 17, 2026
package dependencies
Package suggested but not available for checking: ‘cmdstanr’
package dependencies
Package suggested but not available for checking: ‘cmdstanr’
package dependencies
Package suggested but not available for checking: 'cmdstanr'
WARNING 11 OK · 2 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE Mar 16, 2026
package dependencies
Package suggested but not available for checking: ‘cmdstanr’
package dependencies
Package suggested but not available for checking: ‘cmdstanr’
package dependencies
Package suggested but not available for checking: 'cmdstanr'
NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
package dependencies
Package suggested but not available for checking: ‘cmdstanr’
package dependencies
Package suggested but not available for checking: ‘cmdstanr’
package dependencies
Package suggested but not available for checking: 'cmdstanr'