# ============================================================================== # Generate code lists for Hypertension # Authors: SM Wu & S Picton # Date Created: 2026/04/08 # Date Updated: 2026/04/15 # # Details: # 1) Set up and load data # 2) Search for new relevant med codes # 3) Create updated code lists # 4) Adjust formatting for extraction # # Inputs: # 1) Code_Lists/MASTER_Lists/CPRD_Aurum_Medical_14Oct2025.txt: Aurum medical master code list # 2) Code_Lists/MASTER_Lists/CPRD_GOLD_Medical_14Oct2025.txt: GOLD medical master code list # 3) Code_Lists/Hypertension/Old/Aurum_Hypertension_20240228_Alvin.txt : Old Aurum Hypertension code list # 4) Code_Lists/Hypertension/Old/Gold_Hypertension_20240228_Alvin.txt : Old Gold Hypertension code list # # Final Outputs: # 1) Code_Lists/Hypertension/Aurum_Hypertension_code_list_20260408.txt : Updated Aurum Hypertension code list # 2) Code_Lists/Hypertension/Gold_Hypertension_code_list_20260408.txt : Updated Gold Hypertension code list # 3) Code_Lists/Hypertension/Aurum_Gold_Hypertension_code_list_20260408.txt : Updated combined Aurum and Gold Hypertension code list # ================= 1) Set up and load data ==================================== # Clear memory rm(list = ls()) # Packages library(readr) library(dplyr) library(stringr) library(tidyr) # If working in Data Safe Haven - manually install packages using Artifactory: # bit, bit64, cli, crayon, dplyr, generics, glue, hms, # lifecycle, magrittr, pillar, pkgconfig, purrr, R6, readr, rlang, stringi, # stringr, tibble, tidyr, tidyselect, tzdb, utf8, vctrs, vroom, withr, writexl # ### For running locally # # Set working directory # wd <- "/Volumes/ritd-ag-project-rd00qv-jfhay18/" # VPN connection # # wd <- "//live.rd.ucl.ac.uk/ritd-ag-project-rd00qv-jfhay18/" #Desktop@UCL # setwd(wd) # # # Set input and output paths # path_input <- "Code_Lists/" # path_output <- "Code_Lists/Hypertension/" ### For running in Data Safe Haven # Set working directory wd <- "S:/CDSTP_CPRD_25_005368/" setwd(wd) # Set input and output paths path_input <- "SMI_GLP/Code_Lists/" path_output <- "SMI_GLP/Code_Lists/Hypertension/" ## Load data # Read in Aurum medical dictionary cprd_aurum_medical_raw <- read_delim( paste0(wd, path_input, "MASTER_Lists/CPRD_Aurum_Medical_14Oct2025.txt"), delim = "\t", escape_double = FALSE, col_types = cols(MedCodeId = col_character(), OriginalReadCode = col_character(), CleansedReadCode = col_character(), SnomedCTConceptId = col_character(), SnomedCTDescriptionId = col_character()), trim_ws = TRUE) cprd_aurum_medical <- cprd_aurum_medical_raw %>% select(-Release) %>% rename(term = Term, medcodeid = MedCodeId) %>% mutate(term = str_to_lower(term)) # Read in Gold medical dictionary cprd_gold_medical_raw <- read_delim( paste0(wd, path_input, "MASTER_Lists/CPRD_GOLD_Medical_14Oct2025.txt"), delim = "\t", escape_double = FALSE, col_types = cols(medcode = col_character(), readcode = col_character()), trim_ws = TRUE) cprd_gold_medical <- cprd_gold_medical_raw %>% rename(term = readterm) %>% mutate(term = str_to_lower(term)) # Read in old Hypertension code list from 2024/02/28, setting all col types to character # Aurum aurum_hypertension_old <- read_delim( paste0(wd, path_input, "Hypertension/Old/Aurum_Hypertension_20240228_Alvin.txt"), delim = "\t", escape_double = FALSE, col_types = cols(medcodeid = col_character()), trim_ws = TRUE) # Gold gold_hypertension_old <- read_delim( paste0(wd, path_input, "Hypertension/Old/Gold_Hypertension_20240228_Alvin.txt"), delim = "\t", escape_double = FALSE, col_types = cols(medcode = col_character()), trim_ws = TRUE) # ================= 2) Search for new relevant med codes ======================= # Aurum aurum_hypertension <- cprd_aurum_medical %>% # Inclusion - Hypertension related terms, filter(grepl(paste0("(?i)hypertension|hypertensive|high blood pressure|high diastolic|high systolic"), term)) %>% # Exclusion - Unrelated terms filter(!grepl(paste0("(?i)pulmonary|intracranial|intracranial|ocular|ocular", # Relating to pregnancy "pregnancy|pregnant|obstetric|maternal|pre-eclampsia|gestational|preg.|preg/childb/puerp","maternal", # Relating to family history "family history|fh:|no fh:|no significant family history| no family history| no family history|no family history of|family history|family history of hypertension|family", # Relating to children "child|paediatric|infant|infancy|newborn|fetus|neonate|neonatal","neonatal effect", # Negation "no history of|no h/o:|not to have|resolved|resolved", # Process of care "has-bled|abnormal renal|chads2|cha2ds2-vasc|screening"), term, perl = TRUE)) %>% # Filter out family history codes filter(!grepl("family history:[-_ ]*hypertension", term, ignore.case = TRUE, perl = TRUE)) %>% filter(!grepl("family history[-_ ]*hypertension", term, ignore.case = TRUE, perl = TRUE)) %>% # Filter out neonatal codes filter(!grepl("neonatal[-_ ]*hypertension", term, ignore.case = TRUE, perl = TRUE)) %>% filter(!grepl("neonatal[-_ ]*hypertensive", term, ignore.case = TRUE, perl = TRUE)) %>% # Filter out pulmonary hypertension codes filter(!grepl("pulmonary[-_ ]*hypertension", term, ignore.case = TRUE, perl = TRUE)) # Gold gold_hypertension <- cprd_gold_medical %>% # Inclusion - Hypertension related terms, filter(grepl(paste0("(?i)hypertension|hypertensive|high blood pressure|high diastolic|high systolic"), term)) %>% # Exclusion - Unrelated terms filter(!grepl(paste0("(?i)pulmonary|intracranial|intracranial|ocular|ocular", # Relating to pregnancy "pregnancy|pregnant|obstetric|maternal|pre-eclampsia|gestational|preg.|preg/childb/puerp","maternal", # Relating to family history "family history|fh:|no fh:|no significant family history| no family history| no family history|no family history of|family history|family history of hypertension|family", # Relating to children "child|paediatric|infant|infancy|newborn|fetus|neonate|neonatal","neonatal effect", # Negation "no history of|no h/o:|not to have|resolved|resolved", # Process of care "has-bled|abnormal renal|chads2|cha2ds2-vasc|screening|screen"), term, perl = TRUE)) %>% # Filter out family history codes filter(!grepl("family history:[-_ ]*hypertension", term, ignore.case = TRUE, perl = TRUE)) %>% filter(!grepl("family history[-_ ]*hypertension", term, ignore.case = TRUE, perl = TRUE)) %>% # Filter out neonatal codes filter(!grepl("neonatal[-_ ]*hypertension", term, ignore.case = TRUE, perl = TRUE)) %>% filter(!grepl("neonatal[-_ ]*hypertensive", term, ignore.case = TRUE, perl = TRUE)) %>% # Filter out pulmonary hypertension codes filter(!grepl("pulmonary[-_ ]*hypertension", term, ignore.case = TRUE, perl = TRUE)) ## Comparing with older codelists # New codes not in old list new_aurum <- aurum_hypertension %>% filter(!medcodeid %in% aurum_hypertension_old$medcodeid) new_gold <- gold_hypertension %>% filter(!medcode %in% gold_hypertension_old$medcode) # Old codes not in new old list miss_new_aurum <- aurum_hypertension_old %>% filter(!medcodeid %in% aurum_hypertension$medcodeid) miss_new_gold <- gold_hypertension_old %>% filter(!medcode %in% gold_hypertension$medcode) ## # ================= 3) Create updated code lists =============================== # Create updated code lists # Aurum hypertension_codelist_aurum_new <- aurum_hypertension # Gold hypertension_codelist_gold_new <- gold_hypertension # Save updated code lists write.table(hypertension_codelist_aurum_new, file = paste0(wd, path_output, "Aurum_Hypertension_codelist_20260408.txt"), sep = "\t", row.names = FALSE) write.table(hypertension_codelist_gold_new, file = paste0(wd, path_output, "Gold_Hypertension_codelist_20260408.txt"), sep = "\t", row.names = FALSE) # Combine Aurum and GOLD updated code lists temp_aurum <- hypertension_codelist_aurum_new %>% rename(medcode = medcodeid, readcode = CleansedReadCode) %>% select(medcode, term) temp_gold <- hypertension_codelist_gold_new %>% select(medcode, term) temp_both <- rbind(temp_aurum, temp_gold) aurum_gold_hypertension_new <- temp_both %>% distinct() # # Combine Aurum and GOLD into one file with a column specifying database hypertension_codelist_aurum_new$database <- "Aurum" hypertension_codelist_gold_new$database <- "Gold" hypertension_codelist_aurum_gold_new <- rbind( hypertension_codelist_aurum_new %>% rename(medcode = medcodeid) %>% select(medcode, term, database), hypertension_codelist_gold_new %>% select(medcode, term, database)) # # # Save combined code list write.table(hypertension_codelist_aurum_gold_new, file = paste0(wd, path_output, "Aurum_Gold_Hypertension_codelist_20260408.txt"), sep = "\t", row.names = FALSE)