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).