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A reprex from Thomas Dilling over email:
library(tidyverse) library(tidymodels) library(censored) #> Loading required package: survival library(finetune) library(survival) tidymodels_prefer() data(cancer) lung <- lung %>% drop_na() lung <- lung %>% mutate(survival = Surv(time, status == 2), .keep = 'unused') survival_metrics <- metric_set(concordance_survival, brier_survival) evaluation_time_points <- seq(30, 1020, 30) cv_splits <- vfold_cv(lung, v = 10) lasso_rec <- recipe(survival ~ ., data = lung) %>% update_role(survival, new_role = "outcome") %>% step_novel(all_nominal_predictors()) %>% step_dummy(all_nominal_predictors()) lasso <- proportional_hazards(penalty = tune(), mixture = 1) %>% set_engine('glmnet') %>% set_mode('censored regression') lasso_wf <- workflow() %>% add_recipe(lasso_rec) %>% add_model(lasso) lasso_grid <- grid_space_filling(penalty(), size = 15, type = "max_entropy") lasso_param <- lasso_wf %>% extract_parameter_set_dials() %>% update(penalty = penalty(c(-9, -1))) set.seed(100) lasso_res <- tune_grid(lasso_wf, resamples = cv_splits, grid = lasso_grid, metrics = survival_metrics, eval_time = evaluation_time_points, control = control_grid(save_pred = TRUE)) ctrl_sa <- control_sim_anneal(verbose_iter = TRUE, no_improve = 20L) lasso_sa <- lasso_wf %>% tune_sim_anneal( resamples = cv_splits, metrics = survival_metrics, initial = lasso_res, param_info = lasso_param, eval_time = evaluation_time_points, # Not needed for concordance_survival iter = 50, control = ctrl_sa ) #> Optimizing concordance_survival #> Error in if (!is.na(eval_time) && any(names(res) == ".eval_time")) {: missing value where TRUE/FALSE needed #> ✖ Optimization stopped prematurely; returning current results.
Created on 2024-09-01 with reprex v2.1.0
No issues with tune_grid() or tune_bayes().
tune_grid()
tune_bayes()
The text was updated successfully, but these errors were encountered:
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A reprex from Thomas Dilling over email:
Created on 2024-09-01 with reprex v2.1.0
No issues with
tune_grid()
ortune_bayes()
.The text was updated successfully, but these errors were encountered: