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# System prepended metadata

title: README for test debiasing

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# README for test debiasing

This document describes the protocol for generating debiased prevalence estimates using Test-and-Trace data (Pillars 1+2, LFD and PCR tsts) in combination with REACT randomised surveillance data.

## Inputs

- **REACT study.** {total, positive} test counts aggregated weekly at PHE region level
- **Pillar 1 & 2 test data.** Downloaded from UKHSA EDGE testresults database. We have three testing combinations that we analyse separately: LFD Pillar 2, PCR Pillar 1, PCR Pillar 2

## Outputs



## Method

The approach used to generate debiased prevalence estimates is available in [this paper](https://www.nature.com/articles/s41564-021-01029-0).

We have implemented a few minor changes to the method:

- **Bounded bias.** In order to incorporate time periods where LFD tests returned positivity rates of 1, we upper bound the prior on delta at 20


## Caveats (Data)

- **EDGE deduplication strategy.** For each week, we retain only each individual's final test result for each individual, using (year-month of birth, postcode) as a proxy for individual ID
- **Missing Reporting_Labs.** We retain all Reporting_Labs with value NA (all negative PCR Pillar 2 tests have  missing lab)
- **Immensa lab filtering.** We remove all test results from Immensa labs 


## Caveats (Method)

- REACT may be subject to its own ascertainment bias
-  Full details of methodological caveats are available in the SI  ull 


