COVID-19 impact on mental and physical health

Exploring the indirect effects the COVID-19 public health emergency on the reporting, diagnosis and treatment of mental and physical health conditions. There is particular focus on the potential missed diagnoses as a result of patient's avoiding healthcare settings and the widespread move to remote consultations.

Publication details

Williams R, Jenkins DA, Ashcroft DM, Brown B, Campbell S, Carr MJ, et al. Diagnosis of physical and mental health conditions in primary care during the COVID-19 pandemic: a retrospective cohort study. Lancet Public Heal [Internet]. 2020 Sep;5(10):E543–50. Available from: https://doi.org/10.1016/S2468-2667(20)30201-2

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Instructions

1. Updated codesets are placed in data-extraction/codesets
2. Run node main.js to create the SQL queries necessary for data extraction
3. When on the server execute data-extraction/RunToExtractData.bat to extract the data
4. Data with daily counts ends up in a directory outside of this repo due to small numbers
5. Analysis instructions are below

Analysis

Pre-requisites

1. R installed and bin directory added to the PATH variable - e.g. so that Rscript entered at a command prompt actually does something
2. nodejs installed
3. In root of project execute npm i to install dependencies (none at present but you never know)

Execution

Navigate to the root of the project and execute:

npm run analyse

All outputs appear in the ./outputs directory. Redacted monthly data will be written to the ./data-extraction/data directory. Any counts <10 are replaced with 0s.