From 3fb002a12f8d0e78ea713672dac3e62f6d895a4d Mon Sep 17 00:00:00 2001
From: Kyle Belanger <kyle.belanger@roche.com>
Date: Tue, 31 Jan 2023 15:29:27 -0500
Subject: [PATCH] Update 2-modeling.R
---
ML/2-modeling.R | 14 +++++++++++++-
1 file changed, 13 insertions(+), 1 deletion(-)
diff --git a/ML/2-modeling.R b/ML/2-modeling.R
index 81ae12c..93874f0 100644
--- a/ML/2-modeling.R
+++ b/ML/2-modeling.R
@@ -13,6 +13,7 @@ box::use(
,r = recipes
,wf = workflows
,p = parsnip
+ ,ys = yardstick
)
@@ -48,13 +49,14 @@ table(ds_test$ft4_dia) %>% prop.table()
# random forest -----------------------------------------------------------
+
rf_model <- p$rand_forest(trees = 1900) %>%
p$set_engine("ranger") %>% p$set_mode("classification")
rf_recipe <- r$recipe(ft4_dia ~ . , data = ds_train) %>%
r$update_role(subject_id, new_role = "id") %>%
r$update_role(charttime, new_role = "time") %>%
- r$step_impute_knn(r$all_predictors())
+ r$step_impute_bag(r$all_numeric())
@@ -63,3 +65,13 @@ rf_workflow <- wf$workflow() %>%
wf$add_recipe(rf_recipe)
rf_fit <- p$fit(rf_workflow, ds_train)
+
+rf_predict <- ds_train %>%
+ dplyr::select(ft4_dia) %>%
+ dplyr::bind_cols(
+ predict(rf_fit, ds_train)
+ ,predict(rf_fit, ds_train, type = "prob")
+ )
+
+ys$accuracy(rf_predict, ft4_dia, .pred_class)
+ys$conf_mat(rf_predict, ft4_dia, .pred_class)