From 427d365908088a4b4791f66177bde10bb0e6854e Mon Sep 17 00:00:00 2001
From: Kyle Belanger <kyleb44@hotmail.com>
Date: Fri, 6 Jan 2023 08:46:52 -0500
Subject: [PATCH] Update 0-data_prep.R
---
ML/0-data_prep.R | 38 ++++++++++++++++++++++++++++++++++----
1 file changed, 34 insertions(+), 4 deletions(-)
diff --git a/ML/0-data_prep.R b/ML/0-data_prep.R
index 471395d..63ff9d3 100644
--- a/ML/0-data_prep.R
+++ b/ML/0-data_prep.R
@@ -21,7 +21,8 @@ db <- dbConnect(
,here("ML","data-unshared","mimicDB.sqlite")
)
-
+#item list shows two different numbers for a few tests, second set of items do not have
+# any results that are on the same samples as TSH and Free T4
test_list <- c(
50862 #Albumin
,50863 #Alkaline Phosphatase
@@ -38,7 +39,7 @@ test_list <- c(
,50885 #Bilirubin, Total
,50976 #Protein, Total
,50993 #Thyroid Stimulating Hormone
- ,50995 #Thyroxine (T4), FreE
+ ,50995 #Thyroxine (T4), Free
)
@@ -53,10 +54,39 @@ ds <- dplyr$tbl(db, "labevents") %>%
,names_from = itemid
,values_from = valuenum
) %>%
- dplyr$filter(!is.na(`50993`)) %>%
+ dplyr$filter(!is.na(`50993`) & !is.na(`50995`)) %>%
dplyr$collect()
-ds <- ds %>% dplyr$collect()
+
+ds %>% dplyr$filter(dplyr$across(where(is.numeric), ~!is.na(.x)))
+
+count <- data.frame(colSums(is.na(ds))) %>% tibble::rownames_to_column()
+
+
+testds <- readr::read_csv(
+ here("ML","data-unshared", "labevents.csv")
+ ,col_types = "_d_ddTT_d______"
+ ,n_max = 100
+)
+
+
+
+
+ds1 <- dplyr$tbl(db, "labevents") %>%
+ dplyr$filter(itemid %in% test_list) %>%
+ dplyr$select(-storetime) %>%
+ tidyr$pivot_wider(
+ id_cols = c(subject_id,charttime)
+ ,names_from = itemid
+ ,values_from = valuenum
+ ) %>%
+ dplyr$filter(!is.na(`50993`) & !is.na(`50995`)) %>%
+ dplyr$collect()
+
+count2 <- data.frame(colSums(is.na(ds1))) %>% tibble::rownames_to_column()
+
+counts <- count %>%
+ dplyr$left_join(count2)
# close database ----------------------------------------------------------