EpiNow2 is an R package for estimating the time-varying reproduction number, and growth rates based on underlying latent infections. It is also used to forecast the future course of outbreaks both in terms of forecasting the reproduction number and reported cases. Community support is needed to allow the developers to focus on developing, validating and improving the underlying methodology.
A package review would help identify key pain paints, areas for improvements and provide insights on an interface level that the developers may not have thought of.
Deliberables:
Review all package documentation, high light and fix if possible.
Review the suggested use case/workflow of the package and identify potential issues with the suggested use cases.
Review the package code and suggest improvements for best practice, stability etc (though keep in mind the developers have extremely limited resources at this time and so may not be able to make large scale changes).
Review the documentation provided to on board developers and suggest improvements.
Check the JOSS checklist and highlights outstanding issues.
Optional deliverables:
After highlighting issues providing fixes.
[impact: EpiNow2 is used by the developers, in partnership with the Met office, to produce reproduction number estimates for Covid-19 on a national and subnational basis each day (https://epiforecasts.io/covid/). These estimates are then used by multiple organisations including the WHO and UK government agencies. The package itself is used, both by the developers and by public health agencies, to estimate reproduction numbers that inform policy in multiple countries. On top of this, the package is used to forecast Covid-19 cases, and admissions both for the German and US forecasting hubs and used to answer current questions of interest (such as assessing the impact of firebreak lockdowns in Wales and Northern Ireland (https://github.com/epiforecasts/rt-breakpoints)).]
[originally proposed by @seabbs]
[suggested repo: https://github.com/epiforecasts/EpiNow2 | @seabbs]
[additional notes: ]
EpiNow2 is an R package for estimating the time-varying reproduction number, and growth rates based on underlying latent infections. It is also used to forecast the future course of outbreaks both in terms of forecasting the reproduction number and reported cases. Community support is needed to allow the developers to focus on developing, validating and improving the underlying methodology.
A package review would help identify key pain paints, areas for improvements and provide insights on an interface level that the developers may not have thought of.
Deliberables:
Optional deliverables:
[impact: EpiNow2 is used by the developers, in partnership with the Met office, to produce reproduction number estimates for Covid-19 on a national and subnational basis each day (https://epiforecasts.io/covid/). These estimates are then used by multiple organisations including the WHO and UK government agencies. The package itself is used, both by the developers and by public health agencies, to estimate reproduction numbers that inform policy in multiple countries. On top of this, the package is used to forecast Covid-19 cases, and admissions both for the German and US forecasting hubs and used to answer current questions of interest (such as assessing the impact of firebreak lockdowns in Wales and Northern Ireland (https://github.com/epiforecasts/rt-breakpoints)).] [originally proposed by @seabbs] [suggested repo: https://github.com/epiforecasts/EpiNow2 | @seabbs] [additional notes: ]