NOTE: this repository is now discontinued, please see https://github.com/thibautjombart/nhs_pathways_monitoring for latest updates

Introduction

This repository contains a reportfactory automating the production of routine results for the analysis of potential COVID-19 symptoms reported through England NHS Pathways.

The NHS Pathways dataset describes potential COVID-19 symptoms reported in England through 111 and 999 calls, and 111 online reports. It is updated daily (except weekends), and is freely available via the NHS Digital website.

Initial setup

When initialising the reportfactory, you can load all dependencies using:

## install dependencies (if first time running)
source("scripts/install_devel_packages.R")
reportfactory::install_deps()

Loading the latest extracted datasets

Loading the latest extracted NHS Pathways dataset

When working within this reportfactory, the latest extracted NHS Pathways dataset can be loaded using a helper function. After loading the global factory scripts (in scripts/) using reportfactory::rfh_load_scripts(), the data can be loaded with import_pathways():

## load the global factory scripts
reportfactory::rfh_load_scripts()

## load the latest extracted NHS Pathways dataset
pathways <- import_pathways()
pathways

Alternatively, the path to the latest extracted NHS Pathways data is stored in current_pathways, and the file can be read directly using readRDS() or rio::import():

## load the global factory scripts
reportfactory::rfh_load_scripts()

## use the path to the latest extracted NHS Pathways dataset to read the file
current_pathways

pathways <- readRDS(current_pathways)
pathways

pathways <- rio::import(current_pathways)
pathways

Loading other datasets

The repository also contains COVID-19 daily deaths in England, by NHS region, extracted from the NHS website.

As with NHS Pathways data, the deaths data can be extracted using a helper function, or read directly using readRDS() or rio::import()

## load the global factory scripts
reportfactory::rfh_load_scripts()

## load the latest extracted deaths dataset
deaths <- import_deaths()
deaths

## use the path to the latest extracted deaths dataset to read the file
current_deaths

deaths <- readRDS(current_deaths)
deaths

deaths <- rio::import(current_deaths)
deaths

Compiling the analysis

Generating the figures

The initial analysis can be locally compiled using the nhs_pathways_analysis_2020-05-13.Rmd report in the report_sources/ folder.

reportfactory::compile_report("nhs_pathways_analysis_2020-05-13.Rmd")

All outputs will be generated in the report_outputs/ folder, classified by report name (including the date of the report source, not of the compilation), and then by date and time of compilation.

These outputs are then used to update the clean report.

Generating the report

Once the initial analysis has been locally compiled, the report can be generated using the nhs_pathways_report_2020-05-13.Rmd report in the report_sources/ folder.

reportfactory::compile_report("nhs_pathways_analysis_2020-05-13.Rmd")

Again, all outputs will be generated in the report_outputs/ folder, including the pdf report.

Locally updating datasets

Updating the NHS Pathways dataset

If you wish to locally extract and clean the latest version of the NHS Pathways data from the NHS website, this can be achieved with the clean_latest_pathways_2020-05-13.Rmd report, in the report_sources/ folder. The report can be compiled using:

reportfactory::compile_report("clean_latest_pathways_2020-05-13.Rmd")

Updating the deaths dataset

Similarly, the deaths dataset can also be locally updated using the clean_latest_deaths_2020-05-13.Rmd report.

reportfactory::compile_report("clean_latest_deaths_2020-05-13.Rmd")

License

This work is distributed under MIT License (see LICENSE file).