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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Show all 14 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-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | NOTE |
| 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 details (23 non-OK)
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installed size is 148.8Mb
sub-directories of 1Mb or more:
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extdata 2.8Mb
libs 141.9Mb
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for GNU extensions in Makefiles
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installed package size
installed size is 152.5Mb
sub-directories of 1Mb or more:
doc 2.1Mb
extdata 2.8Mb
libs 145.6Mb
package dependencies
Package suggested but not available for checking: ‘cmdstanr’
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Package unavailable to check Rd xrefs: 'cmdstanr'
for GNU extensions in Makefiles
GNU make is a SystemRequirements.
installed package size
installed size is 13.5Mb
sub-directories of 1Mb or more:
doc 2.1Mb
extdata 2.8Mb
libs 6.7Mb
package dependencies
Package suggested but not available for checking: 'cmdstanr'
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NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 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'