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epiverse-trace / episoap

[Not published - under active development] A Store of Outbreak Analytics Pipelines Provided as Rmarkdown Report Templates
https://epiverse-trace.github.io/episoap/
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Use a line list as default pipeline data #89

Closed joshwlambert closed 5 months ago

joshwlambert commented 1 year ago

Currently the {episoap} transmissibility pipeline uses pre-aggregated COVID data. However, this does not fit with the pipeline's usage of the {linelist} and {incidence2} packages which tag and aggregate line list data.

Replacing the current default data with a line list would better demonstrate the full functionality of the {episoap} pipeline.

pratikunterwegs commented 1 year ago

Taking a look at {linelist} and {incidence2} to understand what they do and what might be required to add them in the pipeline before committing to taking up this issue.

joshwlambert commented 1 year ago

Just to clarify, it's not that the packages are not included, but that a line list data set would better demonstrate their functionality.

Bisaloo commented 1 year ago

I had a look at the linelist data in global.health and it's too incomplete to make a good example in this pipeline.