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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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Missing info in EpiNow2 chunk #141

Closed CarmenTamayo closed 2 months ago

CarmenTamayo commented 2 months ago

@Bisaloo there's a Rmd code chunk that just says "missing for now" in the EpiNow2 section of the template, should this be removed? the code above it does generate the plot with regional estimates so I'm not sure whether this was a typo or if there's actually some information that needs to be added

https://github.com/epiverse-trace/episoap/blob/2b56ffb61ad8dc68325cff3d1b27c86406a279b7/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiNow2.Rmd#L109

Bisaloo commented 2 months ago

The idea was to add a boxplot/mustache plot, such as the same one we are provided in the chunk with the same name in the EpiEstim child document:

https://github.com/epiverse-trace/episoap/blob/a44eda57a04a42fc9a23aaaf29491c42e9e18a10/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiEstim.Rmd#L148-L165

The overall concept was to have a perfect match (or as good as possible) match across the different package options.

CarmenTamayo commented 2 months ago

So should I add this as well? Or was there a blocker for this at the time that I should be aware of? Also, I'm not able to knit the template with EpiNow2 because of a lock file error, but at least on the Rmd I see that the chunk starts with an "Explanation" section that appears to be empty- what did you envision to include here? an overview of the package and how it's used to estimate transmissibility? should I add it too? https://github.com/epiverse-trace/episoap/blob/a44eda57a04a42fc9a23aaaf29491c42e9e18a10/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiNow2.Rmd#L11

Bisaloo commented 2 months ago

So should I add this as well? Or was there a blocker for this at the time that I should be aware of?

As far as I remember, it was mostly a lack of time to do it at the time. It would be great if you can add it.

chunk starts with an "Explanation" section that appears to be empty- what did you envision to include here?

It was added to match perfectly what is present in the i2extras child document. I'm no longer sure what the best solution is here. Maybe this section should be removed from all child documents, including i2extras, in line with what we discussed in https://github.com/epiverse-trace/episoap/issues/120.

CarmenTamayo commented 2 months ago

This has been addressed in #144 by adding a corresponding section of explanations for the other Rmd chunks (EpiNow2, EpiEstim, R0)