properly branched

r_scripts/1112024_try_replace_colnames_scorecsvs.R

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+#Here, we would like to change the Participant Id numbers in the SCORE export repeating data files to BRICK participant Ids. This way, we can upload it to the BRICK castor
+#here we read in the score repeating data files
+library(dplyr)
+
+# Read the subset key table and rename the Participant.Id to BRICK_Id
+subset_key_table <- read.csv("Z:/castor_proof_files/csv_castor/current/brick_subset_key_table102024.csv") %>%
+  rename(BRICK_Id = Participant.Id)
+
+# Read in all of the repeating data files from SCORE #path is for windows machine /mnt/data on linux!.
+# Read in all of the repeating data files from SCORE
+file_paths <- list(
+  visual_hearing = "Z:/score_clinical_manifestationTOBEREVIEWED/SCORE_RADeep-registry__Visual_and_hearing_disease_Medical_History_Clinical_manifestati_export_20240717.csv",
+  acute_complications = "Z:/score_clinical_manifestationTOBEREVIEWED/SCORE_RADeep-registry__Acute_complications_export_20240717.csv",
+  bone_extremities = "Z:/score_clinical_manifestationTOBEREVIEWED/SCORE_RADeep-registry__Bone_and_extremities_Medical_History_Clinical_manifestations_export_20240717.csv",
+  cardiac_pulmonary = "Z:/score_clinical_manifestationTOBEREVIEWED/SCORE_RADeep-registry__Cardiac_and_pulmonary_disease_Medical_History_Clinical_manifest_export_20240717.csv",
+  comorbidities = "Z:/score_clinical_manifestationTOBEREVIEWED/SCORE_RADeep-registry__Comorbidities_export_20240717.csv",
+  endocrinological = "Z:/score_clinical_manifestationTOBEREVIEWED/SCORE_RADeep-registry__Endocrinological_disease_Medical_History_Clinical_manifestation_export_20240717.csv",
+  registry = "Z:/score_clinical_manifestationTOBEREVIEWED/SCORE_RADeep-registry__export_20240717.csv",
+  liver_kidney = "Z:/score_clinical_manifestationTOBEREVIEWED/SCORE_RADeep-registry__Liver_and_kidney_disease_Medical_History_Clinical_manifestation_export_20240717.csv",
+  neurological = "Z:/score_clinical_manifestationTOBEREVIEWED/SCORE_RADeep-registry__Neurological_disease_Medical_History_Clinical_manifestations_export_20240717.csv",
+  specific_treatment = "Z:/score_clinical_manifestationTOBEREVIEWED/SCORE_RADeep-registry__Treatment_Use_of_specific_treatment_or_inclusion_in_Clinical_Tr_export_20240717.csv",
+  chelation_treatment = "Z:/score_clinical_manifestationTOBEREVIEWED/SCORE_RADeep-registry__Treatments_chelation_export_20240717.csv",
+  hydroxyurea_treatment = "Z:/score_clinical_manifestationTOBEREVIEWED/SCORE_RADeep-registry__Treatments_hydroxyurea_export_20240717.csv",
+  visit = "Z:/score_clinical_manifestationTOBEREVIEWED/SCORE_RADeep-registry__Visit_export_20240717.csv"
+)
+
+# Read each file into a data frame and store in df_list
+df_list <- lapply(file_paths, function(path) {
+  read.csv(path, sep = ";", stringsAsFactors = FALSE)
+})
+
+# Rename the first column in each data frame to RADeep_id
+df_list <- lapply(df_list, function(df) {
+  colnames(df)[1] <- "RADeep_id"
+  df
+})
+
+# Merge each data frame with subset_key_table, bringing in BRICK_Id and renaming it to Participant Id
+df_list <- lapply(df_list, function(df) {
+  df %>%
+    left_join(subset_key_table, by = "RADeep_id") %>%  # Join on RADeep_id
+    mutate(`Participant Id` = BRICK_Id) %>%  # Create Participant Id from BRICK_Id
+    select(`Participant Id`, everything(), -BRICK_Id)  # Arrange columns accordingly
+})
+
+# Optionally assign back to original data frame names
+names(df_list) <- names(file_paths)
+
+# Assign back to individual data frames if needed
+list2env(df_list, envir = .GlobalEnv)
+
+# Define the output directory for the updated CSV files
+output_dir <- "Z:/castor_proof_files/csv_castor/current/"
+
+# Ensure the output directory exists
+dir.create(output_dir, showWarnings = FALSE)
+
+# Write each data frame to a CSV file in the output directory
+for (name in names(df_list)) {
+  write.csv(df_list[[name]], file = paste0(output_dir, name, "_updated.csv"), row.names = FALSE)
+}
+
+# Confirm file creation
+cat("CSV files have been created in:", output_dir, "\n")