Old and new regions for cases presents in estimates - UK about covid-rt-estimates HOT 8 CLOSED

Thanks for noticing this Sam, sorry I missed it.

For cases, deaths, and admissions, we need to remove:

• Yorkshire and The Humber
• North East
• West Midlands
• East Midlands

For admissions only, we need to remove:

• United Kingdom

from covid-rt-estimates.

@joeHickson could you clean these folders out from the production server? I think the Cornish internet is not ready for a 20Gb download and I don't have a VM with this loaded at the mo 😸

from covid-rt-estimates.

This is getting fairly urgent. Can anyone look at this please?

I see multiple regions being updated for deaths in a way that I don't understand:

https://github.com/epiforecasts/covid-rt-estimates/tree/master/subnational/united-kingdom/deaths/national

@kathsherratt are there duplicate regions in the data source?

I have removed the UK for admissions.

from covid-rt-estimates.

Certainly the list at the point it's passed to epinow 2 is different:

2020-10-14 01:01:11 INFO Producing estimates for: East of England, England, London, Midlands, North East and Yorkshire, North West, Northern Ireland, Scotland, South East, South West, Wales, United Kingdom
2020-10-15 00:59:27 INFO Producing estimates for: East Midlands, East of England, England, London, North East, North West, Northern Ireland, Scotland, South East, South West, Wales, West Midlands, Yorkshire and The Humber, United Kingdom

We don't have logging of what locations were in the original data.

from covid-rt-estimates.

Is it possible the data source has changed?

from covid-rt-estimates.

The data source seems fine, returning the correct geographies (4 nations + 7 NHS regions) with data present for the correct variables (cases_new, deaths_new, and hosp_new_blend).

data <- covidregionaldata::get_regional_data("uk", nhsregions = TRUE)
unique(data$region)

But it does look like the 2 "new" regions that are only brought in by using the nhsregions = TRUE argument (Midlands; North East & Yorkshire) haven't updated recently, at least for cases (last updated 2 days ago).

Has anything changed with the use of data_args in dataset-list.R? Could it be a change where the argument nhsregions = TRUE doesn't get passed through to covidregionaldata?

from covid-rt-estimates.

let see if that reoslves it

from covid-rt-estimates.

looks like some more bits might have gone astray with the problematic merge of #73

from covid-rt-estimates.