correct interface to fit.probability_calibration() (#49)

Author: simonpcouch

R/adjust-probability-calibration.R

@@ -15,7 +15,6 @@
 #'
 #' @inheritSection adjust_numeric_calibration Data Usage
 #'
-# TODO: see #36
 #' @examplesIf FALSE
 # @examplesIf rlang::is_installed("modeldata")
 #' library(modeldata)
@@ -95,10 +94,10 @@ fit.probability_calibration <- function(object, data, tailor = NULL, ...) {
     eval_bare(
       call2(
         paste0("cal_estimate_", method),
-        .data = data,
+        .data = expr(data),
         # todo: make getters for the entries in `columns`
         truth = tailor$columns$outcome,
-        estimate = tailor$columns$estimate,
+        estimate = tailor$columns$probabilities,
         .ns = "probably"
       )
     )
@@ -116,7 +115,11 @@ fit.probability_calibration <- function(object, data, tailor = NULL, ...) {
 
 #' @export
 predict.probability_calibration <- function(object, new_data, tailor, ...) {
-  probably::cal_apply(new_data, object$results$fit)
+  probably::cal_apply(
+    .data = new_data,
+    object = object$results$fit,
+    pred_class = !!tailor$columns$estimate
+  )
 }
 
 # todo probably needs required_pkgs methods for cal objects

tests/testthat/test-adjust-probability-calibration.R

@@ -15,8 +15,6 @@ test_that("basic adjust_probability_calibration() usage works", {
       adjust_probability_calibration(method = "logistic")
   )
 
-  skip("TODO: cannot run for now due to #36")
-
   expect_no_condition(
     tlr_fit <- fit(
       tlr,
@@ -28,7 +26,7 @@ test_that("basic adjust_probability_calibration() usage works", {
   )
 
   expect_no_condition(
-    predict(tlr_fit, d_test)
+    tlr_pred <- predict(tlr_fit, d_test)
   )
 
   # classes are as expected

tests/testthat/test-utils.R

@@ -17,7 +17,7 @@ test_that("tailor_fully_trained works", {
         fit(
           two_class_example,
           outcome = "truth",
-          estimate = tidyselect::contains("Class"),
+          estimate = predicted,
           probabilities = tidyselect::contains("Class")
         ) %>%
         adjust_probability_threshold(.5)
@@ -31,10 +31,7 @@ test_that("tailor_fully_trained works", {
         fit(
           two_class_example,
           outcome = "truth",
-          # todo: this function requires a different format of `estimate`
-          # and `probabilities` specification than the call below to
-          # be able to fit properly.
-          estimate = tidyselect::contains("Class"),
+          estimate = predicted,
           probabilities = tidyselect::contains("Class")
         )
     )