The goal of codeusage is to make yearly summaries of SNOMED Code Usage in Primary Care and ICD-10 and OPCS Code Usage in Secondary Care in England, published by NHS Digital, available in R for research. The interactive Code Usage Explorer dashboard provides different options to explore these datasets.
The original data is available from NHS Digital at:
Installation
You can install the development version of codeusage like so:
remotes::install_github("ebmdatalab/codeusage")Example
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: 1,523,967 × 7
#> start_date end_date snomed_concept_id description usage active_at_start
#> <date> <date> <chr> <chr> <int> <lgl>
#> 1 2023-08-01 2024-07-31 279991000000102 Short message… 4.41e8 TRUE
#> 2 2023-08-01 2024-07-31 184103008 Patient telep… 1.91e8 TRUE
#> 3 2023-08-01 2024-07-31 428481002 Patient mobil… 1.16e8 TRUE
#> 4 2023-08-01 2024-07-31 423876004 Clinical docu… 7.81e7 TRUE
#> 5 2023-08-01 2024-07-31 72313002 Systolic arte… 6.87e7 TRUE
#> 6 2023-08-01 2024-07-31 1091811000000102 Diastolic art… 6.87e7 TRUE
#> 7 2023-08-01 2024-07-31 1000731000000107 Serum creatin… 4.82e7 TRUE
#> 8 2023-08-01 2024-07-31 60621009 Body mass ind… 4.65e7 TRUE
#> 9 2023-08-01 2024-07-31 1000661000000107 Serum sodium … 4.63e7 TRUE
#> 10 2023-08-01 2024-07-31 1000651000000109 Serum potassi… 4.62e7 TRUE
#> # ℹ 1,523,957 more rows
#> # ℹ 1 more variable: active_at_end <lgl>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.
# Return ICD-10 code usage data
icd10_usage
#> # A tibble: 135,951 × 5
#> start_date end_date icd10_code description usage
#> <date> <date> <chr> <chr> <int>
#> 1 2023-04-01 2024-03-31 A000 Cholera due to Vibrio cholerae 01, bi… 2
#> 2 2023-04-01 2024-03-31 A009 Cholera, unspecified 40
#> 3 2023-04-01 2024-03-31 A010 Typhoid fever 884
#> 4 2023-04-01 2024-03-31 A011 Paratyphoid fever A 139
#> 5 2023-04-01 2024-03-31 A012 Paratyphoid fever B 13
#> 6 2023-04-01 2024-03-31 A013 Paratyphoid fever C 2
#> 7 2023-04-01 2024-03-31 A014 Paratyphoid fever, unspecified 68
#> 8 2023-04-01 2024-03-31 A020 Salmonella enteritis 2165
#> 9 2023-04-01 2024-03-31 A021 Salmonella sepsis 319
#> 10 2023-04-01 2024-03-31 A022 Localized salmonella infections 82
#> # ℹ 135,941 more rowsDataset: OPCS Code Usage in Secondary Care in England
This is the total annual count of each instance that each 4-character OPCS 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/opcs_usage.R.
# Return OPCS code usage data
opcs_usage
#> # A tibble: 107,376 × 5
#> start_date end_date opcs_code description usage
#> <date> <date> <chr> <chr> <int>
#> 1 2023-04-01 2024-03-31 A011 Hemispherectomy 7
#> 2 2023-04-01 2024-03-31 A012 Total lobectomy of brain 36
#> 3 2023-04-01 2024-03-31 A013 Partial lobectomy of brain 134
#> 4 2023-04-01 2024-03-31 A018 Other specified major excision of tiss… 27
#> 5 2023-04-01 2024-03-31 A019 Unspecified major excision of tissue o… 3
#> 6 2023-04-01 2024-03-31 A021 Excision of lesion of tissue of fronta… 1399
#> 7 2023-04-01 2024-03-31 A022 Excision of lesion of tissue of tempor… 971
#> 8 2023-04-01 2024-03-31 A023 Excision of lesion of tissue of pariet… 704
#> 9 2023-04-01 2024-03-31 A024 Excision of lesion of tissue of occipi… 260
#> 10 2023-04-01 2024-03-31 A025 Excision of lesion of tissue of cerebe… 604
#> # ℹ 107,366 more rows