Vignette: pipeline with different data streams

[joshwlambert]

Identify tools, resources and potential blockers to facilitate activities on day 2 & 3.

[finlaycampbell]

https://github.com/epiverse-trace/episoap/blob/main/inst/rmarkdown/templates/transmissibility/skeleton/skeleton.Rmd

[joshwlambert]

Useful Packages:

• episoap
• godataR
• sitrep

Useful Data:

• Data from godataR (.rds and .csv available in google drive here: https://drive.google.com/drive/u/0/folders/1qE2qflcZfFebGC8Ef_WtPJHP0t_N3xTr)
• Data from global.health

Useful scripts:

• various R related scripts developed around Go.Data project which could be streamlined/packaged better:
  https://worldhealthorganization.github.io/godata/R/
• in particular, flex dashboard example or daily sitrep example: https://github.com/WorldHealthOrganization/godata-r-reports
  -these need ALOT of work and are pretty messy.

[joshwlambert]

Plan:

• Select a few data streams
• Document a minimal standard for data
• Get transmissibility pipeline working with multiple data streams
• Write vignette on how to use {episoap} with a novel data stream, useful for field epis to understand how to apply the pipelines
• Add severity pipeline to {episoap}
• Make severity pipeline work with multiple data streams
• Plan and add new pipelines to {episoap}

[joshwlambert]

Documentation on how to add a pipeline to the package.

[sarahollis]

some examples:
https://www.reconlearn.org/post/simulated-evd-early
https://www.reconlearn.org/post/practical-ebola-reconstruction.html

[joshwlambert]

{episoap} R package

[yuriei]

WHO mapping package (aligned with UN/WHO legal requirements for the international boundaries)
https://github.com/whocov/whomapper

[sarahollis]

here is the google doc we can add to:
https://drive.google.com/drive/u/0/folders/1Rj7-1AvxeEeHqLWn-_oxnCTBasBTjZ5N

[CarmenTamayo]

Severity and ascertainment pipeline https://github.com/CarmenTamayo/Applications-Epiverse-pipelines/blob/ctc-edits/Severity_ascertainment_case_studies.Rmd

[joshwlambert]

https://docs.google.com/document/d/1A1_7cJtBMZx7LtUCWyPVCd3fwqvEnR8Jfin6tdYszzs/edit#heading=h.qrsuq5nunybt

https://github.com/joshwlambert/epipipe
https://joshwlambert.github.io/epipipe/