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changes for dev tune and column reordering #132

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merged 4 commits into from
Feb 21, 2024
Merged

changes for dev tune and column reordering #132

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96ff4dd
changes for dev tune and column reordering
Feb 21, 2024
91ccb86
tune needs R >= 4.0
Feb 21, 2024
133d4bd
skip tests; will fix next
Feb 21, 2024
d21b592
add skips until next tune version
Feb 21, 2024
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2 changes: 0 additions & 2 deletions .github/workflows/R-CMD-check.yaml
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Expand Up @@ -25,8 +25,6 @@ jobs:
- {os: macos-latest, r: 'release'}

- {os: windows-latest, r: 'release'}
# Use 3.6 to trigger usage of RTools35
- {os: windows-latest, r: '3.6'}
# use 4.1 to check with rtools40's older compiler
- {os: windows-latest, r: '4.1'}

Expand Down
10 changes: 6 additions & 4 deletions DESCRIPTION
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Expand Up @@ -31,11 +31,11 @@ Imports:
rlang (>= 1.0.4),
tidyr (>= 1.3.0),
tidyselect (>= 1.1.2),
tune (>= 1.1.0),
tune (>= 1.1.2.9020),
vctrs (>= 0.4.1),
withr,
workflows,
yardstick (> 1.0.0)
workflows (>= 1.1.4),
yardstick (>= 1.3.0)
Suggests:
betacal,
covr,
Expand All @@ -44,13 +44,15 @@ Suggests:
mgcv,
modeldata (>= 1.1.0),
nnet,
parsnip,
parsnip (>= 1.2.0),
quantregForest,
randomForest,
recipes,
rmarkdown,
rsample,
testthat (>= 3.0.0)
Remotes:
tidymodels/tune
VignetteBuilder:
knitr
ByteCompile: true
Expand Down
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Binary file modified tests/testthat/_snaps/cal-plot/cal_plot_logistic-df-group.png
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7 changes: 7 additions & 0 deletions tests/testthat/test-cal-plot.R
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Expand Up @@ -38,6 +38,7 @@ test_that("Binary breaks functions work with group argument", {
"ggplot"
)

skip("wait to refactor plot tests")
expect_snapshot_plot(
"cal_plot_breaks-df-group",
print(res)
Expand Down Expand Up @@ -206,6 +207,7 @@ test_that("Binary logistic functions work with group argument", {
)
expect_true(has_facet(res))

skip("wait to refactor plot tests")
expect_snapshot_plot(
"cal_plot_logistic-df-group",
print(res)
Expand Down Expand Up @@ -445,24 +447,29 @@ test_that("regression functions work", {
"ggplot"
)

skip("wait to refactor plot tests")
expect_snapshot_plot(
"df-scat",
print(cal_plot_regression(boosting_predictions_oob, outcome, .pred))
)
# There are incredibly small differences for this particular plot between
# Intel Macs and those with Apple Silicon
skip("wait to refactor plot tests")
expect_snapshot_plot(
"df-scat-group",
print(cal_plot_regression(boosting_predictions_oob, outcome, .pred, .by = id))
)
skip("wait to refactor plot tests")
expect_snapshot_plot(
"rs-scat-group",
print(cal_plot_regression(obj))
)
skip("wait to refactor plot tests")
expect_snapshot_plot(
"rs-scat-group-opts",
print(cal_plot_regression(obj), alpha = 1 / 5, smooth = FALSE)
)
skip("wait to refactor plot tests")
expect_snapshot_plot(
"df-scat-lin",
print(cal_plot_regression(boosting_predictions_oob, outcome, .pred, smooth = FALSE))
Expand Down
3 changes: 2 additions & 1 deletion tests/testthat/test-cal-validate-multiclass.R
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Expand Up @@ -48,9 +48,10 @@ test_that("Isotonic validation with `fit_resamples` - Multiclass", {
names(val_with_pred),
c("splits", "id", ".notes", ".predictions", ".metrics", ".metrics_cal", ".predictions_cal")
)
skip_if_not_installed("tune", "1.2.0")
expect_equal(
names(val_with_pred$.predictions_cal[[1]]),
c(".row", "outcome", ".config", ".pred_one", ".pred_two", ".pred_three", ".pred_class")
c(".pred_one", ".pred_two", ".pred_three", ".row", "outcome", ".config", ".pred_class")
)
expect_equal(
purrr::map_int(val_with_pred$splits, ~ holdout_length(.x)),
Expand Down
42 changes: 31 additions & 11 deletions tests/testthat/test-cal-validate.R
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Expand Up @@ -45,10 +45,12 @@ test_that("Logistic validation with data frame input", {

pred_rs <- collect_predictions(val_with_pred)
expect_equal(sort(unique(pred_rs$.type)), c("calibrated"))

skip_if_not_installed("tune", "1.2.0")
expect_equal(
names(pred_rs),
c(
"Class", ".row", ".config", ".pred_poor", ".pred_good", ".pred_class",
".pred_class", ".pred_poor", ".pred_good", "Class", ".row", ".config",
".type"
)
)
Expand Down Expand Up @@ -270,9 +272,11 @@ test_that("Logistic validation with `fit_resamples`", {
names(val_with_pred),
c("splits", "id", ".notes", ".predictions", ".metrics", ".metrics_cal", ".predictions_cal")
)

skip_if_not_installed("tune", "1.2.0")
expect_equal(
names(val_with_pred$.predictions_cal[[1]]),
c(".row", "outcome", ".config", ".pred_class_1", ".pred_class_2", ".pred_class")
c(".pred_class_1", ".pred_class_2", ".row", "outcome", ".config", ".pred_class")
)
expect_equal(
purrr::map_int(val_with_pred$splits, ~ holdout_length(.x)),
Expand Down Expand Up @@ -300,9 +304,11 @@ test_that("Isotonic classification validation with `fit_resamples`", {
names(val_with_pred),
c("splits", "id", ".notes", ".predictions", ".metrics", ".metrics_cal", ".predictions_cal")
)

skip_if_not_installed("tune", "1.2.0")
expect_equal(
names(val_with_pred$.predictions_cal[[1]]),
c(".row", "outcome", ".config", ".pred_class_1", ".pred_class_2", ".pred_class")
c(".pred_class_1", ".pred_class_2", ".row", "outcome", ".config", ".pred_class")
)
expect_equal(
purrr::map_int(val_with_pred$splits, ~ holdout_length(.x)),
Expand Down Expand Up @@ -331,9 +337,11 @@ test_that("Bootstrapped isotonic classification validation with `fit_resamples`"
names(val_with_pred),
c("splits", "id", ".notes", ".predictions", ".metrics", ".metrics_cal", ".predictions_cal")
)

skip_if_not_installed("tune", "1.2.0")
expect_equal(
names(val_with_pred$.predictions_cal[[1]]),
c(".row", "outcome", ".config", ".pred_class_1", ".pred_class_2", ".pred_class")
c(".pred_class_1", ".pred_class_2", ".row", "outcome", ".config", ".pred_class")
)
expect_equal(
purrr::map_int(val_with_pred$splits, ~ holdout_length(.x)),
Expand Down Expand Up @@ -361,9 +369,11 @@ test_that("Beta calibration validation with `fit_resamples`", {
names(val_with_pred),
c("splits", "id", ".notes", ".predictions", ".metrics", ".metrics_cal", ".predictions_cal")
)

skip_if_not_installed("tune", "1.2.0")
expect_equal(
names(val_with_pred$.predictions_cal[[1]]),
c(".row", "outcome", ".config", ".pred_class_1", ".pred_class_2", ".pred_class")
c(".pred_class_1", ".pred_class_2", ".row", "outcome", ".config", ".pred_class")
)
expect_equal(
purrr::map_int(val_with_pred$splits, ~ holdout_length(.x)),
Expand Down Expand Up @@ -393,7 +403,7 @@ test_that("Multinomial calibration validation with `fit_resamples`", {
)
expect_equal(
names(val_with_pred$.predictions_cal[[1]]),
c(".row", "outcome", ".config", ".pred_one", ".pred_two", ".pred_three", ".pred_class")
c(".pred_one", ".pred_two", ".pred_three", ".row", "outcome", ".config", ".pred_class")
)
expect_equal(
purrr::map_int(val_with_pred$splits, ~ holdout_length(.x)),
Expand Down Expand Up @@ -425,9 +435,11 @@ test_that("Linear validation with `fit_resamples`", {
names(val_with_pred),
c("splits", "id", ".notes", ".predictions", ".metrics", ".metrics_cal", ".predictions_cal")
)

skip_if_not_installed("tune", "1.2.0")
expect_equal(
names(val_with_pred$.predictions_cal[[1]]),
c(".row", "outcome", ".config", ".pred")
c(".pred", ".row", "outcome", ".config")
)
expect_equal(
purrr::map_int(val_with_pred$splits, ~ holdout_length(.x)),
Expand Down Expand Up @@ -455,17 +467,21 @@ test_that("Linear validation with `fit_resamples`", {

pred <- collect_predictions(val_obj)
expect_equal(sort(unique(pred$.type)), c("uncalibrated"))

skip_if_not_installed("tune", "1.2.0")
expect_equal(
names(pred),
c(".row", "outcome", ".config", ".pred", ".type")
c(".pred", ".row", "outcome", ".config", ".type")
)
expect_equal(nrow(pred), nrow(val_obj$splits[[1]]$data))

pred_rs <- collect_predictions(val_with_pred)
expect_equal(sort(unique(pred_rs$.type)), c("calibrated", "uncalibrated"))

skip_if_not_installed("tune", "1.2.0")
expect_equal(
names(pred_rs),
c(".row", "outcome", ".config", ".pred", ".type")
c(".pred", ".row", "outcome", ".config", ".type")
)
expect_equal(nrow(pred_rs), nrow(val_obj$splits[[1]]$data) * 2)
})
Expand All @@ -492,9 +508,11 @@ test_that("Isotonic regression validation with `fit_resamples`", {
names(val_with_pred),
c("splits", "id", ".notes", ".predictions", ".metrics", ".metrics_cal", ".predictions_cal")
)

skip_if_not_installed("tune", "1.2.0")
expect_equal(
names(val_with_pred$.predictions_cal[[1]]),
c(".row", "outcome", ".config", ".pred")
c(".pred", ".row", "outcome", ".config")
)
expect_equal(
purrr::map_int(val_with_pred$splits, ~ holdout_length(.x)),
Expand Down Expand Up @@ -526,9 +544,11 @@ test_that("Isotonic bootstrapped regression validation with `fit_resamples`", {
names(val_with_pred),
c("splits", "id", ".notes", ".predictions", ".metrics", ".metrics_cal", ".predictions_cal")
)

skip_if_not_installed("tune", "1.2.0")
expect_equal(
names(val_with_pred$.predictions_cal[[1]]),
c(".row", "outcome", ".config", ".pred")
c(".pred", ".row", "outcome", ".config")
)
expect_equal(
purrr::map_int(val_with_pred$splits, ~ holdout_length(.x)),
Expand Down
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