Add howto on estimating ascertainment with EpiNow2 - #105
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avallecam
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Thanks @jamesmbaazam for the contribution! I tagged you on comments that I need to have your input to proceed with the suggested changes.
I can take charge of some downstream pending actions:
- create an
estimate-ascertainment/folder - move this entry to this new folder
- add namespace to functions
| # (scale) with a secondary case | ||
| res <- estimate_secondary( | ||
| df, | ||
| obs = obs_opts( |
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@jamesmbaazam a question about the obs argument:
- when used in
estimate_infections()it refers to the % observed reported cases among infections - when used in
estimate_secondary()it refers to the % observed secondary cases among primary cases.
Is this right? Slightly different if you confirm my interpretation, which could be more explicit in the documentation?
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Or does it always refer to the % of observed primary observations?
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Sorry for lagging this entry. I just filled in a discussion with a question I would like to clarify. epiforecasts/EpiNow2#1102
After it, my question would be:
- To estimate the ascertainment rate as done by
{cfr}, defined asascertainment = defined / estimated(as in cfr::estimate_ascertainment()), should we add an extra step to the reprex code? For example, assuming that the prior of Normal(0.2,0.2) was thedefinedCFR.
jamesmbaazam
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Jun 9, 2025
Co-authored-by: James Azam <james.m.azam@gmail.com>
avallecam
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Jun 18, 2025
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June 18, 2025 17:45
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This PR adds a howto guide on how to estimate ascertainment or the fraction of observed cases from a time series of primary and secondary observations.