test_that("fit_selectcox() returns a proper mlsurv_model wrapper", { skip_on_cran() skip_if_not_installed("pec") skip_if_not_installed("survival") df <- survival::veteran Surv <- survival::Surv mod <- fit_selectcox( Surv(time, status) ~ age + celltype + karno, data = df, rule = "aic" ) expect_s3_class(mod, "mlsurv_model") expect_identical(mod$learner, "selectcox") expect_identical(attr(mod, "engine"), "selectCox") expect_true(!is.null(mod$model)) }) test_that("predict_selectcox() returns bounded, monotone survival at requested times", { skip_on_cran() skip_if_not_installed("pec") skip_if_not_installed("survival") df <- survival::veteran Surv <- survival::Surv mod <- fit_selectcox( Surv(time, status) ~ age + celltype + karno, data = df, rule = "aic" ) times <- c(150, 30, 300, 200) newx <- df[1:6, ] pred <- predict_selectcox(mod, newdata = newx, times = times) expect_s3_class(pred, "data.frame") expect_equal(nrow(pred), nrow(newx)) expect_equal(ncol(pred), length(times)) expect_setequal(colnames(pred), paste0("t=", as.character(times))) M <- as.matrix(pred) expect_true(is.numeric(M)) expect_true(all(is.finite(M))) expect_gte(min(M), -1e-12) expect_lte(max(M), 1 + 1e-12) ord <- order(times) M_ord <- M[, paste0("t=", as.character(times[ord])), drop = FALSE] diffs <- t(apply(M_ord, 1, diff)) expect_true(all(diffs <= 1e-8)) }) test_that("predict_selectcox() errors when newdata lacks required predictors", { skip_on_cran() skip_if_not_installed("pec") skip_if_not_installed("survival") df <- survival::veteran Surv <- survival::Surv mod <- fit_selectcox( Surv(time, status) ~ age + celltype + karno, data = df, rule = "aic" ) bad_new <- df[1:3, c("age", "karno")] expect_error( predict_selectcox(mod, newdata = bad_new, times = c(50, 100)), regexp = paste0( "object .* not found|undefined columns|subset.*select|", "do not match|newdata.*missing|terms|model\\.matrix|", 'Value of covariate ".*" not supplied in "newdata"|', "names of independing variables.*do not match" ) ) }) test_that("tune_selectcox() returns a compact grid and refit_best yields a fitted model", { skip_on_cran() skip_if_not_installed("pec") skip_if_not_installed("survival") Surv <- survival::Surv df <- survival::veteran set.seed(2025) rules <- c("aic", "p") res <- tune_selectcox( formula = Surv(time, status) ~ age + celltype + karno, data = df, times = c(60, 180), rules = rules, metrics = c("cindex", "ibs"), folds = 2, seed = 2025, refit_best = FALSE ) expect_s3_class(res, "tuned_surv") expect_true("rule" %in% names(res)) expect_true(all(c("cindex", "ibs") %in% names(res))) expect_true(nrow(res) >= 1) best_mod <- tune_selectcox( formula = Surv(time, status) ~ age + celltype + karno, data = df, times = c(60, 180), rules = rules, metrics = c("cindex", "ibs"), folds = 2, seed = 2025, refit_best = TRUE ) expect_s3_class(best_mod, "mlsurv_model") expect_identical(best_mod$learner, "selectcox") expect_identical(attr(best_mod, "engine"), "selectCox") expect_true(!is.null(attr(best_mod, "tuning_results"))) })