more changes for tidymodels/parsnip#1203

Author: ‘topepo’

DESCRIPTION

@@ -35,7 +35,8 @@ Imports:
     rlang (>= 1.0.0),
     stats,
     tibble (>= 3.1.3),
-    tidyr (>= 1.0.0)
+    tidyr (>= 1.0.0),
+    vctrs
 Suggests:
     aorsf (>= 0.1.2),
     coin,

R/censored-package.R

@@ -62,12 +62,12 @@ utils::globalVariables(
     ".id", ".tmp", "engine", "predictor_indicators", ".strata", "group",
     ".pred_quantile", ".quantile", "interval", "level", ".pred_linear_pred",
     ".pred_link", ".pred_time", ".pred_survival", "next_event_time",
-    "sum_component", "time_interval"
+    "sum_component", "time_interval", "quantile_levels"
   )
 )
 
 # quiet R-CMD-check NOTEs that prodlim is unused
-# (parsnip uses it for all censored regression models 
+# (parsnip uses it for all censored regression models
 # but only has it in Suggests)
 #' @importFrom prodlim prodlim
 NULL

R/survival_reg-data.R

@@ -86,14 +86,14 @@ make_survival_reg_survival <- function() {
     type = "quantile",
     value = list(
       pre = NULL,
-      post = survreg_quant,
+      post = parsnip::matrix_to_quantile_pred,
       func = c(fun = "predict"),
       args =
         list(
           object = expr(object$fit),
           newdata = expr(new_data),
           type = "quantile",
-          p = expr(quantile)
+          p = expr(quantile_levels)
         )
     )
   )
@@ -236,14 +236,14 @@ make_survival_reg_flexsurv <- function() {
     type = "quantile",
     value = list(
       pre = NULL,
-      post = NULL,
+      post = flexsurv_to_quantile_pred,
       func = c(fun = "predict"),
       args =
         list(
           object = rlang::expr(object$fit),
           newdata = rlang::expr(new_data),
           type = "quantile",
-          p = rlang::expr(quantile),
+          p = rlang::expr(quantile_levels),
           conf.int = rlang::expr(interval == "confidence"),
           conf.level = rlang::expr(level)
         )
@@ -393,14 +393,14 @@ make_survival_reg_flexsurvspline <- function() {
     type = "quantile",
     value = list(
       pre = NULL,
-      post = NULL,
+      post = flexsurv_to_quantile_pred,
       func = c(fun = "predict"),
       args =
         list(
           object = rlang::expr(object$fit),
           newdata = rlang::expr(new_data),
           type = "quantile",
-          p = rlang::expr(quantile),
+          p = rlang::expr(quantile_levels),
           conf.int = rlang::expr(interval == "confidence"),
           conf.level = rlang::expr(level)
         )

tests/testthat/test-survival_reg-flexsurv.R

@@ -2,7 +2,7 @@ library(testthat)
 
 test_that("model object", {
   skip_if_not_installed("flexsurv")
-  
+
   set.seed(1234)
   exp_f_fit <- flexsurv::flexsurvreg(
     Surv(time, status) ~ age + ph.ecog,
@@ -149,7 +149,7 @@ test_that("survival probabilities for single eval time point", {
 
 test_that("can predict for out-of-domain timepoints", {
   skip_if_not_installed("flexsurv")
-  
+
   eval_time_obs_max_and_ood <- c(1022, 2000)
   obs_without_NA <- lung[2,]
 
@@ -236,41 +236,28 @@ test_that("quantile predictions", {
   )
 
   expect_s3_class(pred, "tbl_df")
-  expect_equal(names(pred), ".pred")
+  expect_equal(names(pred), ".pred_quantile")
   expect_equal(nrow(pred), 3)
-  expect_true(
-    all(purrr::map_lgl(
-      pred$.pred,
-      ~ all(dim(.x) == c(9, 2))
-    ))
-  )
-  expect_true(
-    all(purrr::map_lgl(
-      pred$.pred,
-      ~ all(names(.x) == c(".quantile", ".pred_quantile"))
-    ))
-  )
-  expect_equal(
-    tidyr::unnest(pred, cols = .pred)$.pred_quantile,
-    do.call(rbind, exp_pred)$est
-  )
+  expect_s3_class(pred$.pred_quantile, c("quantile_pred", "vctrs_vctr", "list"))
+
+  for (.row in 1:nrow(pred)) {
+    expect_equal(
+      unclass(pred$.pred_quantile[.row])[[1]],
+      exp_pred[[.row]]$est
+    )
+  }
 
   # add confidence interval
-  pred <- predict(fit_s,
+  pred_ci <- predict(fit_s,
     new_data = bladder[1:3, ], type = "quantile",
     interval = "confidence", level = 0.7
   )
-  expect_true(
-    all(purrr::map_lgl(
-      pred$.pred,
-      ~ all(names(.x) == c(
-        ".quantile",
-        ".pred_quantile",
-        ".pred_lower",
-        ".pred_upper"
-      ))
-    ))
-  )
+  expect_s3_class(pred_ci, "tbl_df")
+  expect_equal(names(pred_ci), c(".pred_quantile", ".pred_lower", ".pred_upper"))
+  expect_equal(nrow(pred_ci), 3)
+  expect_s3_class(pred_ci$.pred_quantile, c("quantile_pred", "vctrs_vctr", "list"))
+  expect_s3_class(pred_ci$.pred_lower, c("quantile_pred", "vctrs_vctr", "list"))
+  expect_s3_class(pred_ci$.pred_upper, c("quantile_pred", "vctrs_vctr", "list"))
 
   # single observation
   f_pred_1 <- predict(fit_s, bladder[2,], type = "quantile")
@@ -354,7 +341,7 @@ test_that("hazard for single eval time point", {
 
 test_that("`fix_xy()` works", {
   skip_if_not_installed("flexsurv")
-  
+
   lung_x <- as.matrix(lung[, c("age", "ph.ecog")])
   lung_y <- Surv(lung$time, lung$status)
   lung_pred <- lung[1:5, ]
@@ -401,13 +388,13 @@ test_that("`fix_xy()` works", {
     f_fit,
     new_data = lung_pred,
     type = "quantile",
-    quantile = c(0.2, 0.8)
+    quantile_levels = c(0.2, 0.8)
   )
   xy_pred_quantile <- predict(
     xy_fit,
     new_data = lung_pred,
     type = "quantile",
-    quantile = c(0.2, 0.8)
+    quantile_levels = c(0.2, 0.8)
   )
   expect_equal(f_pred_quantile, xy_pred_quantile)
 

tests/testthat/test-survival_reg-flexsurvspline.R

@@ -61,7 +61,7 @@ test_that("survival probability prediction", {
     head(lung),
     type = "survival",
     times = c(0, 500, 1000)
-  ) 
+  )
   if (packageVersion("flexsurv") < "2.3") {
     exp_pred <- exp_pred %>%
       dplyr::rowwise() %>%
@@ -211,59 +211,26 @@ test_that("quantile predictions", {
     set_mode("censored regression") %>%
     fit(Surv(stop, event) ~ rx + size + enum, data = bladder)
   pred <- predict(fit_s, new_data = bladder[1:3, ], type = "quantile")
-
-  set.seed(1)
-  exp_fit <- flexsurv::flexsurvspline(
-    Surv(stop, event) ~ rx + size + enum,
-    data = bladder,
-    k = 1
-  )
-  exp_pred <- summary(
-    exp_fit,
-    newdata = bladder[1:3, ],
-    type = "quantile",
-    quantiles = (1:9) / 10
-  )
-
   expect_s3_class(pred, "tbl_df")
-  expect_equal(names(pred), ".pred")
+  expect_equal(names(pred), ".pred_quantile")
   expect_equal(nrow(pred), 3)
-  expect_true(
-    all(purrr::map_lgl(
-      pred$.pred,
-      ~ all(dim(.x) == c(9, 2))
-    ))
-  )
-  expect_true(
-    all(purrr::map_lgl(
-      pred$.pred,
-      ~ all(names(.x) == c(".quantile", ".pred_quantile"))
-    ))
-  )
-  expect_equal(
-    tidyr::unnest(pred, cols = .pred)$.pred_quantile,
-    do.call(rbind, exp_pred)$est
-  )
+  expect_s3_class(pred$.pred_quantile, c("quantile_pred", "vctrs_vctr", "list"))
+
 
   # add confidence interval
-  pred <- predict(
+  pred_ci <- predict(
     fit_s,
     new_data = bladder[1:3, ],
     type = "quantile",
     interval = "confidence",
     level = 0.7
   )
-  expect_true(
-    all(purrr::map_lgl(
-      pred$.pred,
-      ~ all(names(.x) == c(
-        ".quantile",
-        ".pred_quantile",
-        ".pred_lower",
-        ".pred_upper"
-      ))
-    ))
-  )
+  expect_s3_class(pred_ci, "tbl_df")
+  expect_equal(names(pred_ci), c(".pred_quantile", ".pred_lower", ".pred_upper"))
+  expect_equal(nrow(pred_ci), 3)
+  expect_s3_class(pred_ci$.pred_quantile, c("quantile_pred", "vctrs_vctr", "list"))
+  expect_s3_class(pred_ci$.pred_lower, c("quantile_pred", "vctrs_vctr", "list"))
+  expect_s3_class(pred_ci$.pred_upper, c("quantile_pred", "vctrs_vctr", "list"))
 
   # single observation
   f_pred_1 <- predict(fit_s, bladder[2,], type = "quantile")
@@ -284,7 +251,7 @@ test_that("hazard prediction", {
     head(lung),
     type = "hazard",
     times = c(0, 500, 1000)
-  ) 
+  )
   if (packageVersion("flexsurv") < "2.3") {
     exp_pred <- exp_pred %>%
       dplyr::rowwise() %>%
@@ -409,13 +376,13 @@ test_that("`fix_xy()` works", {
     f_fit,
     new_data = lung_pred,
     type = "quantile",
-    quantile = c(0.2, 0.8)
+    quantile_levels = c(0.2, 0.8)
   )
   xy_pred_quantile <- predict(
     xy_fit,
     new_data = lung_pred,
     type = "quantile",
-    quantile = c(0.2, 0.8)
+    quantile_levels = c(0.2, 0.8)
   )
   expect_equal(f_pred_quantile, xy_pred_quantile)
 
@@ -438,7 +405,7 @@ test_that("`fix_xy()` works", {
 
 test_that("can handle case weights", {
   skip_if_not_installed("flexsurv")
-  
+
   # flexsurv engine can only take weights > 0
   set.seed(1)
   wts <- runif(nrow(lung))

tests/testthat/test-survival_reg-survival.R

@@ -122,16 +122,22 @@ test_that("prediction of survival time quantile", {
     fit(Surv(time, status) ~ age + sex, data = lung)
 
   exp_quant <- predict(res$fit, head(lung), p = (2:4) / 5, type = "quantile")
-  exp_quant <- apply(exp_quant, 1, function(x) {
-    tibble::tibble(.quantile = (2:4) / 5, .pred_quantile = x)
-  })
-  exp_quant <- tibble::tibble(.pred = exp_quant)
-  obs_quant <- predict(res, head(lung), type = "quantile", quantile = (2:4) / 5)
+  obs_quant <- predict(res, head(lung), type = "quantile", quantile_levels = (2:4) / 5)
 
-  expect_equal(as.data.frame(exp_quant), as.data.frame(obs_quant))
+  expect_s3_class(obs_quant, "tbl_df")
+  expect_equal(names(obs_quant), ".pred_quantile")
+  expect_equal(nrow(obs_quant), 6)
+  expect_s3_class(obs_quant$.pred_quantile, c("quantile_pred", "vctrs_vctr", "list"))
+
+  for (.row in 1:nrow(obs_quant)) {
+    expect_equal(
+      unclass(obs_quant$.pred_quantile[.row])[[1]],
+      exp_quant[.row,]
+    )
+  }
 
   # single observation
-  f_pred_1 <- predict(res, lung[1, ], type = "quantile")
+  f_pred_1 <- predict(res, lung[1, ], type = "quantile", quantile_levels = .5)
   expect_identical(nrow(f_pred_1), 1L)
 })
 
@@ -213,13 +219,13 @@ test_that("`fix_xy()` works", {
     f_fit,
     new_data = lung_pred,
     type = "quantile",
-    quantile = c(0.2, 0.8)
+    quantile_levels = c(0.2, 0.8)
   )
   xy_pred_quantile <- predict(
     xy_fit,
     new_data = lung_pred,
     type = "quantile",
-    quantile = c(0.2, 0.8)
+    quantile_levels = c(0.2, 0.8)
   )
   expect_equal(f_pred_quantile, xy_pred_quantile)