Update 1-data-exploration.R

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$read_rds(
+ds0 <- readr$read_rds(here("ML","data-unshared","ds_final.RDS"))
-  here("ML","data-unshared","ds_high_tsh.RDS")
-  )
-
-ds_low_tsh_raw <- readr$read_rds(
-  here("ML","data-unshared","ds_low_tsh.RDS")
-  )
-
 
 # data manipulation -------------------------------------------------------
 
@@ -54,31 +29,21 @@ 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 %>%
+ds1 <- ds0 %>%
-  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$rename(!!!test_list_names) %>%
   dplyr$select(-FT4, -subject_id, -charttime) %>%
-  dplyr$relocate(gender, anchor_age)
+  dplyr$mutate(dplyr$across(
-
+    ft4_dia
-
+    , ~factor(., levels = c("Hypo", "Non-Hypo", "Normal TSH", "Hyper", "Non-Hyper")
-ds_low_tsh <- ds_low_tsh_raw %>%
+              )
-  dplyr$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)
-
 
 
 # basic visualization -----------------------------------------------------
 
 #summary Table
-#use this instead of making myself
+
-summary_table <- function(ds){
+summary_tbl <- ds1 %>%
-  table <- ds %>%
   gtsummary$tbl_summary(
     by = ft4_dia
     ,missing = "no"
@@ -100,23 +65,8 @@ summary_table <- function(ds){
   gtsummary$modify_header(label = "**Variable**") %>%
   gtsummary$modify_spanning_header(gtsummary$all_stat_cols() ~ "**Free T4 Diagnostic**")
 
-  return(table)
+# summary_tbl
 
-  }
-
-# 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$tbl_merge(
-  tbls = list(high_table_summary, low_table_summary)
-  ,tab_spanner = c(
-    "**Elevated TSH** \n Free T4 Diagnostic"
-    ,"**Decreased TSH** \n Free T4 Diagnostic"
-    )
-  ) %>%
-  gtsummary$as_flex_table()
 
 
 # correlation plot