10012019 pm updates

DAWBA_database_and_deletions.R

@@ -27,11 +27,11 @@ if (exists("master_IRTA_screens_latest")==FALSE) {
   print("master current screens tracker already imported")
 }
 
-if (exists("master_IRTA_old_screens_latest")==FALSE) {
-  master_IRTA_old_screens_latest <- read_excel(paste0(IRTA_tracker_location, "OLD_REFERRALS_DATABASE.xlsx"))
+if (exists("master_IRTA_oldest_screens_latest")==FALSE) {
+  master_IRTA_oldest_screens_latest <- read_excel(paste0(IRTA_tracker_location, "OLD_REFERRALS_DATABASE.xlsx"))
   date_variabes <- c("DOB", "Screening_Start_Date", "Referral_Date", "Consent_Date", "Clinical_Visit_Date", "Clinicals_date", "Overall_date")
   for(i in seq_len(max_tasks)) { date_variabes <- c(date_variabes, paste0("Task", i, "_Date"))}
-  master_IRTA_old_screens_latest[date_variabes] <- lapply(master_IRTA_old_screens_latest[date_variabes], as.Date)
+  master_IRTA_oldest_screens_latest[date_variabes] <- lapply(master_IRTA_oldest_screens_latest[date_variabes], as.Date)
   rm(i, date_variabes)
 } else {
   print("master old referrals tracker already imported")
@@ -55,7 +55,7 @@ master_current_screen_identifiers <- master_IRTA_screens_latest %>%
          Parent_e_consented, Child_e_assented, Parent_DAWBA_completed, Child_DAWBA_completed, DAWBA_completed) %>% 
   mutate(Source = "Current screens") %>% filter(!is.na(DAWBA_ID) | !is.na(PLUSID))
 
-master_old_screen_identifiers <- master_IRTA_old_screens_latest %>% 
+master_old_screen_identifiers <- master_IRTA_oldest_screens_latest %>% 
   select(FIRST_NAME, LAST_NAME, Initials, DAWBA_ID, PLUSID, SDAN, IRTA_tracker, Participant_Type2, 
          Clinical_Visit_Date, Screening_Start_Date, Referral_Date, Overall_date, 
          Eligible, Eligibility_notes, Scheduling_status, Scheduling_status_notes, 

IRTA_Merge_Code.R

@@ -191,7 +191,7 @@ master_IRTA_reordered <- master_IRTA_reordered %>% select(-Clinical_Visit_Code2,
 irta_tracker_columns <- read_excel(paste0(IRTA_tracker_location, "other_data_never_delete/irta_tracker_columns.xlsx"))
 master_IRTA_latest <- master_IRTA_reordered %>% select(irta_tracker_columns$include) %>% arrange(Initials, Clinical_Visit_Date)
 master_IRTA_screens_latest <- master_IRTA_screens_reordered %>% select(irta_tracker_columns$include) %>% arrange(Initials, Referral_Date)
-master_IRTA_old_screens_latest <- master_IRTA_old_screens_reordered %>% select(irta_tracker_columns$include) %>% arrange(Referral_Date)
+master_IRTA_oldest_screens_latest <- master_IRTA_old_screens_reordered %>% select(irta_tracker_columns$include) %>% arrange(Referral_Date)
 
 ####################Chris's here..... 
 
@@ -378,50 +378,50 @@ MID_missing[of_interest] <- lapply(MID_missing[of_interest], na_if, '666')
 MID_missing %>% write_xlsx(paste0(IRTA_tracker_location,"MID_check.xlsx")) # if file empty, everything is perfect 
 
 ######################################################################################
-#######Adding MRI QC information
-
-MEG_tasks <- c("MEG_MMI", "Booster", "RL_GNG")
-
-for(i in seq_along(MEG_tasks)) {
-  iter <- as.numeric(i)
-  # iter=1
-
-  temp_MEG_data <- read_excel(paste0(MEG_tracker_location, "MEG_Tracker.xlsx"), sheet = MEG_tasks[iter]) %>% 
-    mutate_all(as.character) %>% mutate(MEG_tab=meg_task_name) 
-  assign(paste0("task_", iter, "_meg_data"), temp_MEG_data) 
-
-}
-
-# merge & tidy up
-
-rm(temp_MEG_data)
-meg_sets <- ls(pattern="_meg_data")
-meg_sets <- mget(meg_sets)
-meg_combined <- reduce(meg_sets, full_join) %>% rename(Participant_Type = "Group") %>% rename(Task_Date = "taskDate") %>% 
-  rename(Task_Time = "taskTime") %>% rename(SEX = "Sex") %>% rename(Age_at_visit = "Age") %>% rename(IRTA_tracker = "IRTA Contact") %>% 
-  rename(TI_moved = "T1 moved to MEG directory") %>% rename(T1_notes = "T1 Image Notes")
-
-meg_reshape_master = data.frame(matrix(ncol = 23, nrow = 0))
-x <- c("Initials", "SDAN", "MRN", "SEX", "Age_at_visit", "Participant_Type", "MEG_tab", "IRTA_tracker", "Experimenter1", "Experimenter2", 
-       "Photo_PII_Removal", "Earnings", "Scan_Notes", "Scheduling_Notes", "Recent_MPRAGE", 
-       "TI_moved", "T1_notes", "GNGNotes", "Task_Name", "Task_Number", "Task_Date", "Task_Time", "Include")
-colnames(meg_reshape_master) <- x
-
-for(j in seq_len(max_MEG)) {
-  iter <- as.numeric(j)
-  # iter=1
-
-  meg_reshape <- meg_combined %>% 
-      select(Initials, SDAN, MRN, SEX, Age_at_visit, Participant_Type, MEG_tab, IRTA_tracker, Experimenter1, Experimenter2, 
-             Photo_PII_Removal, Earnings, Scan_Notes, Scheduling_Notes, Recent_MPRAGE, TI_moved, T1_notes, GNGNotes, 
-             Task_Date, Task_Time, paste0("Task", iter, "_Name"), paste0("Task", iter, "_Number"), paste0("Task", iter, "_Include")) 
-
-    names(meg_reshape)[names(meg_reshape) == paste0("Task", iter, "_Name")] <- "Task_Name"
-    names(meg_reshape)[names(meg_reshape) == paste0("Task", iter, "_Number")] <- "Task_Number"
-    names(meg_reshape)[names(meg_reshape) == paste0("Task", iter, "_Include")] <- "Include"
-
-    meg_reshape_master <- merge.default(meg_reshape_master, meg_reshape, all=TRUE)
-  }
+#######Adding MEG QC information
+
+# MEG_tasks <- c("MEG_MMI", "Booster", "RL_GNG")
+# 
+# for(i in seq_along(MEG_tasks)) {
+#   iter <- as.numeric(i)
+#   # iter=1
+#   
+#   temp_MEG_data <- read_excel(paste0(MEG_tracker_location, "MEG_Tracker.xlsx"), sheet = MEG_tasks[iter]) %>% 
+#     mutate_all(as.character) %>% mutate(MEG_tab=meg_task_name) 
+#   assign(paste0("task_", iter, "_meg_data"), temp_MEG_data) 
+#   
+# }
+# 
+# # merge & tidy up
+# 
+# rm(temp_MEG_data)
+# meg_sets <- ls(pattern="_meg_data")
+# meg_sets <- mget(meg_sets)
+# meg_combined <- reduce(meg_sets, full_join) %>% rename(Participant_Type = "Group") %>% rename(Task_Date = "taskDate") %>% 
+#   rename(Task_Time = "taskTime") %>% rename(SEX = "Sex") %>% rename(Age_at_visit = "Age") %>% rename(IRTA_tracker = "IRTA Contact") %>% 
+#   rename(TI_moved = "T1 moved to MEG directory") %>% rename(T1_notes = "T1 Image Notes")
+# 
+# meg_reshape_master = data.frame(matrix(ncol = 23, nrow = 0))
+# x <- c("Initials", "SDAN", "MRN", "SEX", "Age_at_visit", "Participant_Type", "MEG_tab", "IRTA_tracker", "Experimenter1", "Experimenter2", 
+#        "Photo_PII_Removal", "Earnings", "Scan_Notes", "Scheduling_Notes", "Recent_MPRAGE", 
+#        "TI_moved", "T1_notes", "GNGNotes", "Task_Name", "Task_Number", "Task_Date", "Task_Time", "Include")
+# colnames(meg_reshape_master) <- x
+# 
+# for(j in seq_len(max_MEG)) {
+#   iter <- as.numeric(j)
+#   # iter=1
+#   
+#   meg_reshape <- meg_combined %>% 
+#       select(Initials, SDAN, MRN, SEX, Age_at_visit, Participant_Type, MEG_tab, IRTA_tracker, Experimenter1, Experimenter2, 
+#              Photo_PII_Removal, Earnings, Scan_Notes, Scheduling_Notes, Recent_MPRAGE, TI_moved, T1_notes, GNGNotes, 
+#              Task_Date, Task_Time, paste0("Task", iter, "_Name"), paste0("Task", iter, "_Number"), paste0("Task", iter, "_Include")) 
+#     
+#     names(meg_reshape)[names(meg_reshape) == paste0("Task", iter, "_Name")] <- "Task_Name"
+#     names(meg_reshape)[names(meg_reshape) == paste0("Task", iter, "_Number")] <- "Task_Number"
+#     names(meg_reshape)[names(meg_reshape) == paste0("Task", iter, "_Include")] <- "Include"
+#     
+#     meg_reshape_master <- merge.default(meg_reshape_master, meg_reshape, all=TRUE)
+#   }
 
 # meg_reshape_master %>% write_xlsx(paste0(IRTA_tracker_location,"meg_tracker_rough.xlsx")) 
 
@@ -453,8 +453,8 @@ master_IRTA_screens_latest %>% write_xlsx(paste0(backup_location,"REFERRAL_AND_S
 ######################################################################################
 #######Saving Old Screens Dataset
 
-master_IRTA_old_screens_latest %>% write_xlsx(paste0(IRTA_tracker_location,"OLD_REFERRALS_DATABASE.xlsx"))
-master_IRTA_old_screens_latest %>% write_xlsx(paste0(backup_location,"OLD_REFERRALS_DATABASE","_",todays_date_formatted,".xlsx"))
+master_IRTA_oldest_screens_latest %>% write_xlsx(paste0(IRTA_tracker_location,"OLD_REFERRALS_DATABASE.xlsx"))
+master_IRTA_oldest_screens_latest %>% write_xlsx(paste0(backup_location,"OLD_REFERRALS_DATABASE","_",todays_date_formatted,".xlsx"))
 
 #####Removing unnecessary variables
 

Update_databases_master_script.R

@@ -5,7 +5,7 @@ rm(list = ls()) # command to clear all variables from R environment
 # directories -------------------------------------------------------------
 
 # what device are you running this script on? 
-computer = 'mac' # set this to either 'mac' or 'pc' or 'other' (Georgia = W:/ as I have string mounted differently)
+computer = 'pc' # set this to either 'mac' or 'pc' or 'other' (Georgia = W:/ as I have string mounted differently)
 
 if (computer=="pc") {
   string = 'W:/'
@@ -73,6 +73,7 @@ suppressPackageStartupMessages(library(purrr))
 suppressPackageStartupMessages(library(tidyverse))
 suppressPackageStartupMessages(library(shiny))
 suppressPackageStartupMessages(library(knitr))
+suppressPackageStartupMessages(library(ggpubr))
 
 # things to check and may need to modify before running -------------------