Include 2m timespan in Nextstrain GISAID and open profiles#957
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- Replicate logic for "6m" profile for "2m" profile - Use narrower bandwidth for "2m" frequencies - Update Markdown description to table out builds
- Replicate logic for "6m" profile for "2m" profile - Use narrower bandwidth for "2m" frequencies - Update Markdown description to table out builds
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Description of proposed changes
This PR extends the previous logic of splitting out
6mandall-timetimespans from PR #910 to include a new2mtimespan.2mwas chosen over1mto allow "logistic growth" calculation using the previous 6 weeks of frequencies pivots to work without modification.With this narrow of timespans there is some unavoidable funny interaction with how
augur filtersubsamples based on--vpm, ie viruses per month. We have common situations where if current date is say May 15 we end up withaugur filterto equally sample viruses from March, April and May categoriesso that March and May have 2 weeks for sampling of X viruses and April has 4 weeks for sampling of X viruses. This results in more densely sampled, in terms of viruses per day, months of March and May compared to April.
This effect will be more pronounced in scenarios where current date is, say, May 28, and so X viruses are sampled in 3 days in March and 30 days in April.
To fully address this we'd need to extend
augur filterto have the option of per-week sampling categories in addition to per-month sampling categories. Or perhaps some continuous specification. However, I don't think this is too big of an issue in terms of the current PR and it's something we can refine once Augur is updated.cc @victorlin @huddlej for Augur issue: nextstrain/augur#960
Testing
Trial builds are available at:
Release checklist
docs/src/reference/change_log.mdin this pull request to document these changes by the date they were added.After merging of this PR, we should:
manifest_guest.jsonto allowing viewing of2mdatasets