diff --git a/ML/2-modeling.R b/ML/2-modeling.R index 07c5f25..675dd7a 100644 --- a/ML/2-modeling.R +++ b/ML/2-modeling.R @@ -144,3 +144,25 @@ rf_reg_predict <- reg_train %>% dplyr::bind_cols( predict(rf_base_reg_fit, reg_train) ) + +reg_metrics(rf_reg_predict, truth = FT4, estimate = .pred) + +rf_reg_tune_model <- p$rand_forest(trees = tune(), mtry = tune(), min_n = tune()) %>% + p$set_engine("ranger") %>% p$set_mode("regression") + +rf_reg_pred <- dplyr::select(reg_train, -FT4, -subject_id, -charttime) + +rf_reg_param <- p$extract_parameter_set_dials(rf_reg_tune_model) %>% + update(mtry = d$finalize(d$mtry(), rf_reg_pred))z + +data_fold_reg <- rsamp$vfold_cv(reg_train, v = 5) + +# takes around 1 hr to run grid search. saving best params manaually +rf_reg_tune <- rf_reg_workflow %>% + tune::tune_grid( + data_fold + ,grid = rf_reg_param %>% d$grid_regular() + ) + + + diff --git a/chapter3.qmd b/chapter3.qmd index ec01092..020f70f 100644 --- a/chapter3.qmd +++ b/chapter3.qmd @@ -68,7 +68,8 @@ All data handling and modeling were performed using R and R Studio. The current #| label: tbl-platform-info #| tbl-cap: Session Info R Environment #| echo: false -#| #| message: false +#| message: false +#| #| warning: false df_session_platform <- devtools::session_info()$platform %>% unlist(.) %>% @@ -90,6 +91,7 @@ knitr::kable( #| tbl-cap: Package Info R Environment #| echo: false #| message: false +#| warning: false df_session_packages <- devtools::session_info(include_base = TRUE)$packages %>% @@ -99,7 +101,7 @@ df_session_packages <- devtools::session_info(include_base = TRUE)$packages %>% colnames(df_session_packages) <- c("Package", "Loaded Version", "Date") -used_packages <-renv::dependencies() %>% dplyr::select(2) +used_packages <-renv::dependencies(progress = FALSE) %>% dplyr::select(2) df_session_packages <- df_session_packages %>% dplyr::filter(Package %in% used_packages$Package)