https://github.com/epiforecasts/covid19.lfd.england

SARS-CoV-2 prevalence in at LTLA level and in educational institutions in England according to LFD testing.
https://github.com/epiforecasts/covid19.lfd.england

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

• Host: GitHub
• URL: https://github.com/epiforecasts/covid19.lfd.england
• Owner: epiforecasts
• License: mit
• Created: 2021-03-04T12:22:38.000Z (over 5 years ago)
• Default Branch: main
• Last Pushed: 2022-06-09T11:40:43.000Z (about 4 years ago)
• Last Synced: 2025-06-08T03:44:03.663Z (about 1 year ago)
• Language: R
• Homepage:
• Size: 51.2 MB
• Stars: 3
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

Awesome Lists containing this project

README

          
---

output: github_document

---

```{r, echo = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "README-"

)

Title <- "LFD prevalence in England"

```

# LFD prevalence in England

This data visualises the latest LFD positivy data published as part of the [Weekly statistics for NHS Test and Trace](https://www.gov.uk/government/collections/nhs-test-and-trace-statistics-england-weekly-reports).

### Latest LFD positive prevalence at LTLA level

![](figure/lfd_last_10_weeks.svg)

![](figure/lfd_last_10_weeks_regions.svg)

![](figure/lfd_last_10_weeks_maps.svg)

### Latest LFD positive prevalence in educational settings

Approximate periods during which schools were closed are shaded dark.

![](figure/lfd_testing.svg)

# 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,  _`r Title`_. Available at .

### How to download or install

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

```{r gh-installation, eval = FALSE}

# install.packages("devtools")

remotes::install_github("sbfnk/covid19.lfd.england")

```

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

```{r lfd, eval = FALSE}

source(system.file(package = "covid19.lfd.england",

                   file.path("scripts", "lfd.r")))

res

```

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

```{r lfd_copy, eval = FALSE}

file.copy(system.file(package = "covid19.lfd.england",

                      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.