This repository is aimed at sharing the R code underlying the joint Strategy Unit / British Heart Foundation (BHF) project to visualise socio-economic inequalities along the CHD pathway
The project included development of a new tool, built using Shiny and aimed at helping Integrated Care Boards (ICBs) get an overview of the points on the care pathway where inequalities emerge and are amplified.
In this repository we aim to provide key sections of code to facilitate re-use on similar projects.
The first two sections of published code are the RII calculations and the calculations that assign GP practices into IMD deciles.
The next code to be published will be the shiny app and the code required to generate the RDS needed for the shiny app.
RII Calculations:
The code rii_calculations.R can be used to calculate the RII with lower and upper confidence intervals and with a confidence interval determined within the code
The input data for this stage of the process is the rds activity_by_type_decile_stg1_testdata.rds
This data has a row for each IMD decile. The first column is the IMD decile number, the second column is the total GP list size for that decile. Each of the other columns is the total activity for that metric and decile. In this example there are 32 metrics.
This test dataset has been created using a random number generator with data items in a range similar to the original dataset.
The output of this stage of the process is sii_table which contains one row per metric and columns for SII, UCI, LCI, RII, UCI_RII, LCI_RII and RR
Assign GP practices into IMD deciles:
The code calculate_gpprac_imd_deciles.R takes three xlsx files as inputs and generates a GP practice list with each practice assigned to an IMD decile and a July-2022 ICB.
The three input files are
- patients_by_lsoa_to_gp.xlsx
The file here is from January 2020, used in this project as the GP practice list sizes timeframe is consistent with much of the data used for the metrics and is also pre-pandemic. The file contains practice list sizes split by LSOA. The latest version of this file can be obtained from :
- imd_2019.xlsx
This file contains the IMD 2019 scores, ranks and deciles for each 2011 LSOA and can be obtained from:
- gp-reg-pat-prac-map-jul22.xlsx
This file maps each GP practice to a July 2022 ICB
The output of this code is a patient weighted GP practice IMD.
This code makes use of regular expressions. More details about them can be found in this NHS-R blog here:
https://nhsrcommunity.com/code-snippets-regular-expressions/
Strategy Unit / British Heart Foundation (BHF) project:
The tool is available here: https://connect.strategyunitwm.nhs.uk/content/b05b649b-511d-4921-9069-2a7a62d694dd/
The accompanying report including methodology and a recording of a webinar about the tool is available here: https://www.bhf.org.uk/-/media/files/publications/research/bhf_visualising-socio-economic-inequalities-in-chd-progression-and-pathways_sept2022.pdf?rev=e43c10defd7a4579a2795887d6728b37&hash=C3933086783DC0E35F4341FEADD087DA
Here is an example of the visualisation used in the tool to display the data generated using the RII calculations
