README.Rmd

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# opencodes

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The goal of `opencodes` is to make yearly summaries of **SNOMED Code Usage in Primary Care** and **ICD-10 and OPCS-4 Code Usage in Secondary Care** in England, published by NHS Digital, available in R for research.
The interactive [OpenCodes Shiny App](https://bennettoxford.github.io/opencodes/articles/app.html) provides different options to explore these datasets.  
The original data is available from NHS Digital at:

-   [SNOMED Code Usage in Primary Care](https://digital.nhs.uk/data-and-information/publications/statistical/mi-snomed-code-usage-in-primary-care)
-   [ICD-10 and OPCS-4 Code Usage in Secondary Care](https://digital.nhs.uk/data-and-information/publications/statistical/hospital-admitted-patient-care-activity)

## Installation

You can install the development version of `opencodes` like so:

``` r
remotes::install_github("bennettoxford/opencodes")
```

## Main functions of the `opencodes` R package

- **Datasets:**
  - `snomedct_usage`: SNOMED CT code usage dataset
  - `icd10_usage`: ICD-10 code usage dataset
  - `opcs4_usage`: OPCS-4 code usage dataset
- **Functions:**
   - `get_codelist()`: Imports a codelists from [www.opencodelists.org](https://www.opencodelists.org/)
   - `run_app()`: Launches interactive OpenCodes Shiny App locally

## Example

```{r load-pkg}
# Load opencodes package
library(opencodes)
```

### Dataset: SNOMED Code Usage in Primary Care in England

This is only a selection of the full dataset published by NHS Digital, for the data pre-processing see `/data-raw/snomed_code_usage.R`.

```{r snomed-usage}
# Return SNOMED code usage data
snomed_usage
```

### Dataset: ICD-10 Code Usage in Secondary Care in England

This is the total annual count of the Finished Consultant Episodes (FCE) listing each 4-character ICD-10 code either in primary or secondary diagnosis position in the Hospital Episode Statistics in England.

This is only a selection of the full dataset published by NHS Digital, for the data pre-processing see `/data-raw/icd10_usage.R`.

```{r icd10-usage}
# Return ICD-10 code usage data
icd10_usage
```

### Dataset: OPCS-4 Code Usage in Secondary Care in England

This is the total annual count of each instance that each 4-character OPCS-4 code is listed across all primary and secondary procedure positions in the Finished Consultant Episodes (FCE) of the Hospital Episode Statistics in England.

This is only a selection of the full dataset published by NHS Digital, for the data pre-processing see `/data-raw/opcs4_usage.R`.

```{r opcs-4-usage}
# Return OPCS-4 code usage data
opcs4_usage
```