From de69edfecce3c1d3cdaf745e9d7692b24052dbdf Mon Sep 17 00:00:00 2001
From: Kyle Belanger <kyleb44@hotmail.com>
Date: Fri, 6 Jan 2023 15:48:47 -0500
Subject: [PATCH] Update 0-data_prep.R

---
 ML/0-data_prep.R | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/ML/0-data_prep.R b/ML/0-data_prep.R
index 1388461..930a110 100644
--- a/ML/0-data_prep.R
+++ b/ML/0-data_prep.R
@@ -60,6 +60,17 @@ test_list_bmp <- c(
 
 # load data ---------------------------------------------------------------
 
+# load patients first to add to lab values
+patients <- dplyr$tbl(db, "patients") %>%
+  dplyr$select(-anchor_year, -anchor_year_group, -dod) %>%
+  dplyr$collect()
+
+#this function is failing if run as part of the DB query
+# Recoding Male = 1, Female = 2
+
+patients <- patients %>%
+  dplyr$mutate(dplyr$across(gender, ~dplyr$recode(gender, "M" = 1, "F" = 2)))
+
 # most likely will not use this as there are not as many complete rows.  However
 # gathering it just in case.
 # first is using specimen id, usable data set is using chart time as it appears
@@ -90,7 +101,8 @@ ds_cmp <- dplyr$tbl(db, "labevents") %>%
 
 #this keeps failing if run as part of the above query.  Moving here to keep going
 # keeps only rows that have values for all columns
-ds_cmp <- ds_cmp %>% dplyr$filter(dplyr$if_all(.fns = ~!is.na(.)))
+ds_cmp <- ds_cmp %>% dplyr$filter(dplyr$if_all(.fns = ~!is.na(.))) %>%
+  dplyr$left_join(patients, by = c("subject_id" = "subject_id"))
 
 
 ds_bmp <- dplyr$tbl(db, "labevents") %>%
@@ -107,6 +119,10 @@ ds_bmp <- dplyr$tbl(db, "labevents") %>%
 ds_bmp <- ds_bmp %>% dplyr$filter(dplyr$if_all(.fns = ~!is.na(.)))
 
 
+
+
+
+
 # close database ----------------------------------------------------------
 
 dbDisconnect(db)