HUNePi results are not being reported in lineage_stats CSV download

PoonLab / covizu

Rapid analysis and visualization of coronavirus genome variation

https://filogeneti.ca/CoVizu/

MIT License

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HUNePi results are not being reported in lineage_stats CSV download #524

Closed ArtPoon closed 3 months ago

ArtPoon commented 3 months ago

Clicking on the CSV button associated with the time-scaled tree (left panel) yields the columns:

lineage
mean.diffs
clock.residual
num.cases
num.variants
min.coldate
max.coldate
mean.coldate

We should also be able to report the predicted number of infections at least. We can also report the summary statistics that go into the HUNePi model:

number of unsampled nodes
Shannon entropy
effective population size (coalescent)
nucleotide diversity (pi)

ArtPoon commented 3 months ago

Reporting predicted number of infections (pred.cases) for now.