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Truncation in UK test positive estimates. #88

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seabbs opened this issue Oct 15, 2020 · 6 comments
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Truncation in UK test positive estimates. #88

seabbs opened this issue Oct 15, 2020 · 6 comments
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@seabbs
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seabbs commented Oct 15, 2020 •
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Looking at UK test positive estimates looks like delay to report has increased and our real time estimates are now biased downwards in some regions. @kathsherratt have you seen any data changes? May need to increase the time lag for this dataset only in order to avoid this for now. @joeHickson that should be possible now right?
@seabbs seabbs changed the title Truncation in U, Truncation in UK test positive estimates. Oct 15, 2020
@seabbs seabbs added the bug Something isn't working label Oct 15, 2020
@joeHickson
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joeHickson commented Oct 16, 2020 •
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Yes - add truncation = 123 to the dataset list.
Tangent: Should we also expose the 12 week number in the same way for completeness? it seems odd to have param for one side of the window but not the other. If so I'll pop open a low priority ticket.

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seabbs commented Oct 16, 2020

Great - yes I think that is a good idea but as you say low priority.

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seabbs commented Oct 18, 2020

This is now critical. Looking at the UK page it appears that Rt is decreasing for test-positive cases. We need to know if this is due to truncation or is a real signal. @kathsherratt any progress on data changes?

@joeHickson can you open a dummy PR indicating how to set truncation for just UK data sets (each one likely needs to be different).

Unfortunately, I am on annual leave until Thursday so not available but happy to make these changes/do the exploration if no one else has any time.

kathsherratt added a commit that referenced this issue Oct 18, 2020
@kathsherratt
Add truncation for UK
799795c 
Aims to address issue #88 by increasing truncation to 5 days in the UK test-positive cases data. Deaths and admissions Rts don't look like they are suffering the same issue so no changes there.

Discussed this with @sbfnk, where we reviewed UK data and recent estimates of delays from test to report in a large UK study. Decision was to truncate at 5 days: truncation at 3 days looks insufficient, 4 days is enough to capture most of the data, plus 1 day feed through into the public PHE dataset.

@joeHickson - from what I can see in the code it looks like all I need to do here is add an extra `truncation` parameter, that gets fed through into the cleaning functions (where the default param is set to 3). I have opened this PR to do this - would that work? (Great if so!)
@kathsherratt kathsherratt mentioned this issue Oct 18, 2020
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@joeHickson joeHickson moved this from To do to Review in progress in rt-estimates kanbanish Oct 19, 2020
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raised the tangent as #102

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@seabbs can I close this with the merge of #97?

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seabbs commented Oct 22, 2020

yes! thanks for work on this everyone.

@seabbs seabbs closed this as completed Oct 22, 2020
rt-estimates kanbanish automation moved this from Review in progress to Done Oct 22, 2020
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