12042019 am updates

fixing DAWBA duplications

DAWBA_database_and_deletions.R

@@ -2,8 +2,6 @@
 #***********DAWBA = diagnostic information from participant screening
 
 # to do: 
-# dawba deletions 
-# bdd information
 
 # Loading patient info ----------------------------------------------------
 
@@ -115,6 +113,7 @@ DAWBA_Archive <- read_excel(paste0(database_location, "other_data_never_delete/d
 dawba_combined <- merge.default(DAWBA_Archive, DAWBA_Data_Download_raw, all=TRUE) %>% 
   filter(sid !="234110") %>% filter(sid !="234111") %>% filter(sid !="234112") %>% filter(sid !="234113") %>% filter(sid !="None")
 fill_names <- dawba_combined %>% select(-sid) %>% colnames()
+dawba_combined[fill_names] <- lapply(dawba_combined[fill_names], na_if, "")
 dawba_combined <- dawba_combined %>% 
   group_by(sid) %>%
   fill(., names(fill_names), .direction = "down") %>%
@@ -134,8 +133,6 @@ DAWBA_Data_Download <- dawba_combined %>% select(dawba_columns$new_name) %>% arr
 
 # Clean up -------------------------------------------
 
-count_na <- function(x) sum(is.na(x))
-
 DAWBA_Data_Download$DAWBA_SEX[DAWBA_Data_Download$DAWBA_SEX==1] <- 'MALE'
 DAWBA_Data_Download$DAWBA_SEX[DAWBA_Data_Download$DAWBA_SEX==2] <- 'FEMALE'
 
@@ -280,17 +277,21 @@ s_bdd_combined <- s_bdd_combined %>% mutate(s_dawba_bdd_diag = (as.numeric(s_daw
 
 all_bdd_combined <- merge.default(s_bdd_combined, p_bdd_combined, all=TRUE)
 fill_names <- all_bdd_combined %>% select(-DAWBA_ID) %>% colnames()
+all_bdd_combined[fill_names] <- lapply(all_bdd_combined[fill_names], na_if, "")
 all_bdd_combined <- all_bdd_combined %>% group_by(DAWBA_ID) %>% 
   fill(., names(fill_names), .direction = "down") %>%
   fill(., names(fill_names), .direction = "up") %>%
   distinct(., .keep_all = TRUE) %>% ungroup()
 
 dawba_w_names <- merge.default(dawba_w_names, all_bdd_combined, all=TRUE) 
+fill_names <- dawba_w_names %>% select(-DAWBA_ID, -matches("date"), -matches("Date"), -DOB) %>% colnames()
+dawba_w_names[fill_names] <- lapply(dawba_w_names[fill_names], na_if, "")
 fill_names <- dawba_w_names %>% select(-DAWBA_ID) %>% colnames()
 dawba_w_names <- dawba_w_names %>% group_by(DAWBA_ID) %>% 
   fill(., names(fill_names), .direction = "down") %>%
   fill(., names(fill_names), .direction = "up") %>%
-  distinct(., .keep_all = TRUE) %>% ungroup()
+  arrange(DAWBA_ID, dawba_logins) %>% slice(1) %>% 
+  ungroup()
 
 # Exporting the database --------------------------------------------------
 

Reports/Research_meeting_numbers.Rmd

@@ -169,7 +169,15 @@ if (exists("Psychometrics_treatment")==FALSE) {
 }
 
 if (exists("MEG_mprage")==FALSE) {
-        MEG_mprage <- read_excel(paste0(IRTA_tracker_location,"QCing/MEG_need_mprage.xlsx"))
+  
+        meg_mprage_file <- list.files(path = paste0(IRTA_tracker_location, "QCing/"), pattern = "^MEG_need_mprage", all.files = FALSE,
+                                 full.names = FALSE, recursive = FALSE,
+                                 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)
+        meg_mprage_file_time <- file.mtime(paste0(IRTA_tracker_location, "QCing/", meg_mprage_file)) %>% as.Date()
+        meg_mprage_combined <- tibble(File=c(meg_mprage_file), Date=c(meg_mprage_file_time)) %>% 
+          arrange(desc(Date)) %>% slice(1)
+        MEG_mprage <- read_excel(paste0(IRTA_tracker_location, "QCing/", meg_mprage_combined[1]))
+        
 } else {
         print("MEG MPRAGE missing info already imported")
 }
@@ -851,7 +859,7 @@ current_inpatients %>% kable(., col.names = c("Initials", "Last Week Recorded",
 rm(referrals_table3a, screens_table2, screens_current_table, ready_2_review, scheduled, scheduling_table2, protocol_table2, 
    inpatients_table, combined, meg_mmi_table2, meg_mmi_upcoming, bloods_table2, 
    current_outpatients, current_inpatients, outpatients, outpatients_table, inpatients, family_hist_table2, 
-   supreme_table, meg_mprage_missing, MEG_mprage, diag_mid_3_table, fu_dates, mid_long)
+   supreme_table, meg_mprage_missing, diag_mid_3_table, fu_dates, mid_long)
 rm(list=ls(pattern="denominator_"))
 rm(list=ls(pattern="numerator_"))