epiforecasts / covid19.lfd.england

SARS-CoV-2 prevalence in at LTLA level and in educational institutions in England according to LFD testing.

LFD prevalence in England

This data visualises the latest LFD positivy data published as part of the Weekly statistics for NHS Test and Trace.

Latest LFD positive prevalence at LTLA level

Latest LFD positive prevalence in educational settings

Approximate periods during which schools were closed are shaded dark.

LFD mass testing in English schools - additional evidence of high test specificity

This repository also contains the data and code for our note:

Funk S, Flasche S, LFD prevalence in England. Available at https://cmmid.github.io/topics/covid19/mass-testing-schools.html.

How to download or install

The code is installed as an R package, covid19.lfd.education, from GitHub with:

# install.packages("devtools")
remotes::install_github("sbfnk/covid19.lfd.education")

To re-create the results, run the script in inst/scripts/lfd.r:

source(system.file(package = "covid19.lfd.education",
                   file.path("scripts", "lfd.r")))
res

To make changes, just create a copy of lfd.r locally and edit this:

file.copy(system.file(package = "covid19.lfd.education",
                      file.path("scripts", "lfd.r"),
                      "my_code_dir/lfd.r"))

Documentation for the estimate_min_specificity function, which is used to estimate the lower bound of specificity, can be found using ?estimate_min_specificity.

Copyright notice

Contains shapefiles from the Office for National Statistics licensed under the Open Government Licence v.3.0. Contains OS data © Crown copyright and database right 2022.