From 66f213bc5a4fc592baf821429ca0f23a057e6fae Mon Sep 17 00:00:00 2001
From: Kyle Belanger <kyleb44@hotmail.com>
Date: Sat, 21 Jan 2023 07:44:35 -0500
Subject: [PATCH] Update 1-data-exploration.R

---
 ML/1-data-exploration.R | 112 +++++++++++-----------------------------
 1 file changed, 31 insertions(+), 81 deletions(-)

diff --git a/ML/1-data-exploration.R b/ML/1-data-exploration.R
index a3412f0..ac3742c 100644
--- a/ML/1-data-exploration.R
+++ b/ML/1-data-exploration.R
@@ -17,36 +17,11 @@ box::use(
 
 # globals -----------------------------------------------------------------
 
-test_list_names <- c(
-   "BUN"   = "51006"
-   ,"CA"   = "50893"
-   ,"CO2"  = "50882"
-   ,"CL"   = "50902"
-   ,"CREA" = "50912"
-   ,"GLU"  = "50931"
-   ,"K"    = "50971"
-   ,"NA"   = "50983"
-   ,"TSH"  = "50993"
-   ,"FT4"  = "50995"
-   ,"RBC"  = "51279"
-   ,"WBC"  = "51300"
-   ,"HCT"  = "51221"
-   ,"HGB"  = "51222"
-   ,"PLT"  = "51265"
-)
-
 
 
 # load data ---------------------------------------------------------------
 
-ds_high_tsh_raw <-   readr$read_rds(
-  here("ML","data-unshared","ds_high_tsh.RDS")
-  )
-
-ds_low_tsh_raw <- readr$read_rds(
-  here("ML","data-unshared","ds_low_tsh.RDS")
-  )
-
+ds0 <- readr$read_rds(here("ML","data-unshared","ds_final.RDS"))
 
 # data manipulation -------------------------------------------------------
 
@@ -54,69 +29,44 @@ ds_low_tsh_raw <- readr$read_rds(
 # using the FT4 Referance range low as the cut off (0.93)
 
 
-ds_high_tsh <- ds_high_tsh_raw %>%
-  dplyr$mutate(ft4_dia = dplyr$if_else(`50995` < 0.93, TRUE, FALSE)) %>%
-  #can rename with a vector using either of these
-  # dplyr$rename_with(~names(test_list_names), dplyr$all_of(test_list_names))
-  dplyr$rename(!!!test_list_names) %>%
+ds1 <- ds0 %>%
   dplyr$select(-FT4, -subject_id, -charttime) %>%
-  dplyr$relocate(gender, anchor_age)
-
-
-ds_low_tsh <- ds_low_tsh_raw %>%
-  dplyr$mutate(ft4_dia = dplyr$if_else(`50995` > 1.7, TRUE, FALSE)) %>%
-  #can rename with a vector using either of these
-  # dplyr$rename_with(~names(test_list_names), dplyr$all_of(test_list_names))
-  dplyr$rename(!!!test_list_names) %>%
-  dplyr$select(-FT4, -subject_id, -charttime) %>%
-  dplyr$relocate(gender, anchor_age)
-
+  dplyr$mutate(dplyr$across(
+    ft4_dia
+    , ~factor(., levels = c("Hypo", "Non-Hypo", "Normal TSH", "Hyper", "Non-Hyper")
+              )
+    )
+  )
 
 
 # basic visualization -----------------------------------------------------
 
 #summary Table
-#use this instead of making myself
-summary_table <- function(ds){
-  table <- ds %>%
-    gtsummary$tbl_summary(
-      by = ft4_dia
-      ,missing = "no"
-      ,type = gtsummary$all_continuous() ~ "continuous2"
-      ,label = list(
-        gender ~ "Gender"
-        ,anchor_age ~ "Age"
-        )
-      ,statistic = gtsummary$all_continuous() ~ c(
-        "{N_miss}"
-        ,"{median} ({p25}, {p75})"
-        ,"{min}, {max}"
-        )
-      ) %>%
-    gtsummary$bold_labels() %>%
-    gtsummary$add_stat_label(
-      label = gtsummary$all_continuous() ~ c("Missing", "Median (IQR)", "Range")
-        ) %>%
-    gtsummary$modify_header(label = "**Variable**") %>%
-    gtsummary$modify_spanning_header(gtsummary$all_stat_cols() ~ "**Free T4 Diagnostic**")
 
-  return(table)
-
-  }
-
-# create both tables
-high_table_summary <- summary_table(ds_high_tsh)
-low_table_summary <- summary_table(ds_low_tsh)
-
-# merge tables
-merged_summary_table <- gtsummary$tbl_merge(
-  tbls = list(high_table_summary, low_table_summary)
-  ,tab_spanner = c(
-    "**Elevated TSH** \n Free T4 Diagnostic"
-    ,"**Decreased TSH** \n Free T4 Diagnostic"
-    )
+summary_tbl <- ds1 %>%
+  gtsummary$tbl_summary(
+    by = ft4_dia
+    ,missing = "no"
+    ,type = gtsummary$all_continuous() ~ "continuous2"
+    ,label = list(
+      gender ~ "Gender"
+      ,anchor_age ~ "Age"
+      )
+    ,statistic = gtsummary$all_continuous() ~ c(
+      "{N_miss}"
+      ,"{median} ({p25}, {p75})"
+      ,"{min}, {max}"
+      )
+    ) %>%
+  gtsummary$bold_labels() %>%
+  gtsummary$add_stat_label(
+    label = gtsummary$all_continuous() ~ c("Missing", "Median (IQR)", "Range")
   ) %>%
-  gtsummary$as_flex_table()
+  gtsummary$modify_header(label = "**Variable**") %>%
+  gtsummary$modify_spanning_header(gtsummary$all_stat_cols() ~ "**Free T4 Diagnostic**")
+
+# summary_tbl
+
 
 
 # correlation plot