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maternal_VE_study/BronchStop_screening_logs_analysis.R

+##Script to create recruitment flowchart for BronchStop VE manuscript##
+##            Thomas Williams, University of Edinburgh               ##
+##                       January 2025                                ##
+
+#load packages
+library(readxl)
+library(dplyr)
+library(tidyverse)
+
+#set working directory
+setwd("TBC")
+
+#create list of files 
+file_list <- list.files(path="TBC")
+
+#create empty dataframe
+screening_log_df <- data.frame()
+
+#loop to read in data, specify columns you want 
+for (i in 1:length(file_list)){
+  temp_data <- read_excel(file_list[i], range = cell_cols("A:G"))
+  print(file_list[i])
+  screening_log_df <- rbind(screening_log_df, temp_data) 
+}
+
+
+#change column names
+screening_log_tidy_headers <-  screening_log_df %>% 
+                               rename( vaccine_eligible = `Vaccine eligible infant?* (Y/N)             (if NO, data not required)`) %>%
+                               rename( consented = `Mother Consented Y/N`) %>%
+                               rename( reason_not_consented = `If Mother Not Consented,  Reason`) %>%
+                               rename( ID = `BRONCHSTART ID (If applicable)`) 
+  
+
+#convert all lower case to upper case
+screening_log_tidy_headers$consented <- toupper(screening_log_tidy_headers$consented)
+
+
+#screen out cases were not eligible for Bronchstop and those that are yet to be contacted, often contain phrase "call next week or similar"
+screening_log_BronchStop <- screening_log_tidy_headers %>%
+                            filter(vaccine_eligible == "Y") %>%
+                            filter_at(vars(consented), all_vars(!is.na(.))) %>%
+                            filter(!grepl("still to contact",Notes)) %>%
+                            filter(!grepl("HAS PIS still trying to contact",Notes)) %>%
+                            filter(!grepl("to be contacted",Notes)) %>%
+                            filter(!grepl("For a call next week",Notes))  
+
+#now look at reasons for exclusion 
+flowchart_results_screening  <- screening_log_BronchStop %>%
+                                group_by(consented, reason_not_consented, Notes)%>% 
+                                count(consented) 
+
+#now create table for flowchart 
+flowchart_for_paper <- screening_log_BronchStop %>%
+                       group_by(consented, reason_not_consented) %>% 
+                       count(consented) 
+
+#write to file
+write.csv(flowchart_for_paper, file = "TBC")
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