clinicalActivity: Clinical Activity in England

The goal of clinicalActivity is to make yearly summaries of SNOMED Code Usage in Primary Care and Hospital Admitted Patient Care Activity published by NHS Digital available in R for research. The original data is available from NHS Digital at:

Installation

You can install the development version of clinicalActivity like so:

remotes::install_github("milanwiedemann/clinicalActivity")

Example

# Load clinicalActivity package
library(clinicalActivity)

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.

# Return SNOMED code usage data
snomed_usage
#> # A tibble: 1,366,513 × 7
#>    start_date end_date   snomed_concept_id description     usage active_at_start
#>    <date>     <date>     <chr>             <chr>           <int> <lgl>          
#>  1 2011-08-01 2012-07-31 163020007         On examinatio… 5.80e7 TRUE           
#>  2 2011-08-01 2012-07-31 163030003         On examinatio… 4.01e7 TRUE           
#>  3 2011-08-01 2012-07-31 163031004         On examinatio… 4.00e7 TRUE           
#>  4 2011-08-01 2012-07-31 1000731000000107  Serum creatin… 2.02e7 TRUE           
#>  5 2011-08-01 2012-07-31 162763007         On examinatio… 1.98e7 TRUE           
#>  6 2011-08-01 2012-07-31 1020291000000106  Glomerular fi… 1.93e7 TRUE           
#>  7 2011-08-01 2012-07-31 1000661000000107  Serum sodium … 1.86e7 TRUE           
#>  8 2011-08-01 2012-07-31 1000651000000109  Serum potassi… 1.86e7 TRUE           
#>  9 2011-08-01 2012-07-31 1022431000000105  Haemoglobin e… 1.81e7 TRUE           
#> 10 2011-08-01 2012-07-31 1022541000000102  Total white c… 1.80e7 TRUE           
#> # ℹ 1,366,503 more rows
#> # ℹ 1 more variable: active_at_end <lgl>

Dataset: Hospital Admitted Patient Care Activity

This is only a selection of the full dataset published by NHS Digital, for the data pre-processing see /data-raw/icd10_code_usage.R.

# Return ICD-10 diagnosis code usage data
icd10_usage
#> # A tibble: 33,893 × 5
#>    start_date end_date   icd10_code description                            usage
#>    <date>     <date>     <chr>      <chr>                                  <int>
#>  1 2022-04-01 2023-03-31 A00.0      Cholera due to Vibrio cholerae 01, bi…     3
#>  2 2022-04-01 2023-03-31 A00.9      Cholera, unspecified                      23
#>  3 2022-04-01 2023-03-31 A01.0      Typhoid fever                            657
#>  4 2022-04-01 2023-03-31 A01.1      Paratyphoid fever A                       71
#>  5 2022-04-01 2023-03-31 A01.2      Paratyphoid fever B                       13
#>  6 2022-04-01 2023-03-31 A01.4      Paratyphoid fever, unspecified            28
#>  7 2022-04-01 2023-03-31 A02.0      Salmonella enteritis                    1762
#>  8 2022-04-01 2023-03-31 A02.1      Salmonella sepsis                        243
#>  9 2022-04-01 2023-03-31 A02.2      Localized salmonella infections           74
#> 10 2022-04-01 2023-03-31 A02.8      Other specified salmonella infections     37
#> # ℹ 33,883 more rows

Interactive Code Usage Explorer

The interactive tool is available online at https://milanwiedemann.shinyapps.io/codeexplorer/ or by launching the Shiny app locally using:

# Open Shiny App to explore code usage interactively
run_explore_activity()