README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

# CHD (Congenital Heart Disease) codes

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This repository contains the SNOMED codes referred to in the NHSR Community 
webinar [Unveiling Congenital Heart Disease and Comorbidities using Primary Care data](https://www.youtube.com/embed/vSekPvgwJKY?si=1a9OpLPIwGE6Fkhj) 
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:

```{r}
library(readr)
library(janitor) # cleans the column names by removing spaces and makes all lower case

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:

```{r}
library(dplyr)

chd_codes <- chd_codes |> 
  mutate(snomed_concept_id_formatted = as.numeric(snomed_concept_id))
```