This repository contains the SNOMED codes referred to in the NHSR Community webinar Unveiling Congenital Heart Disease and Comorbidities using Primary Care data presented by James Partington on 10 July 2024.
The data is an extract of the SNOMED reference page from the CHD Power BI tool developed by the Cheshire and Merseyside Health and Care Partnership in conjunction with the Cheshire CHD in Primary Care Group and shared with kind permission from James Partington and colleagues.
Copyright: Cheshire and Wirral Partnership NHS Foundation Trust, Cheshire and Merseyside Health and Care Partnership
The full list of codes in the csv has been provided to the CHD Clinical Reference Group and is subject to their ongoing review, plus ongoing review by the Cheshire CHD in Primary Care Group
To import this csv file into R:
library(readr)
library(janitor) # cleans the column names by removing spaces and makes all lower case
#>
#> Attaching package: 'janitor'
#> The following objects are masked from 'package:stats':
#>
#> chisq.test, fisher.test
chd_codes <- read_csv("data/chd-codes.csv",
col_types = cols(`SNOMED Concept ID` = col_character())) |>
clean_names()Note that the column SNOMED Concept ID (converted with the janitor
package to snomed_concept_id) is recognised by R as a number so
appears in scientific notation. The code above sets the ID to character
so all the characters show.
If you wish to have this column as numbers use the following dplyr code:
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
chd_codes <- chd_codes |>
mutate(snomed_concept_id_formatted = as.numeric(snomed_concept_id))