Code and codelists for "Cohort studies on 71 different adverse health outcomes among people with atopic eczema in UK primary care data"

How to run

1. Open the R console and call renv::restore() to install the required R packages.
2. Provide a paths.R file in the paths/ folder (see README)
3. Call library(targets) and tar_make() to run the pipeline.

How to inspect targets

• Call tar_read(target) to retrieve a specified target.
• Call tar_visnetwork(targets_only = TRUE) to visualise the pipeline.

Working with CPRD Aurum Define & Extract system

No real data is provided in this repository. CPRD Aurum data is provided via a 2-step process: First, the codes from the relevant codelist need to be provided to define a cohort of exposed individuals (the files are created as [...]_codes_for_define.txt). Second, a list of patids needs to be provided to extract all data for these individuals (the list of patids is created as patids_for_extract.txt).

Typical run time and hardware requirements

With dummy data the pipeline takes approximately 5 minutes to complete on a normal (ca 2023) desktop or laptop computer. With real CPRD Aurum data, the pipeline may take more than 1 week to complete when branches are not run in parallel. Approximately 64 GB of RAM are required.

Files

File	Purpose
_targets.R	Declares the targets pipeline.
R/	Contains R scripts with functions to be used in the pipeline.
codelists/	Contains all codelists (and some that were not used).
dummy_data/	When the pipeline is run, dummy data will be placed here.
output/	When the pipeline is run, outputs will be placed here.
sensitive_output/	When the pipeline is run, sensitive outputs will be placed here (lists for CPRD Aurum define and extract).
paths/	To run the pipeline, the paths.R file needs to be placed here (see README).
renv.lock	The renv lock file that specifies all package versions.