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Pull request review commenttidymodels/recipes

Add `keep_original_cols` to `step_kpca()`

 test_that('No kPCA comps', {     tibble::tibble(terms = paste0("X", 2:6), id = "")   ) })+++test_that('keep_original_cols works', {++  skip_if_not_installed("dimRed")+  skip_if_not_installed("kernlab")++  kpca_rec <- rec %>%+    step_kpca(X2, X3, X4, X5, X6, id = "", keep_original_cols = TRUE)++  kpca_trained <- prep(kpca_rec, training = tr_dat, verbose = FALSE)++  pca_pred <- bake(kpca_trained, new_data = te_dat, all_predictors())++  expect_equal(+    colnames(pca_pred),+    c("X2", "X3", "X4", "X5", "X6",+      "kPC1", "kPC2", "kPC3", "kPC4", "kPC5")+  )++})++test_that('can prep recipes with no keep_original_cols', {+  skip_if_not_installed("dimRed")+  skip_if_not_installed("kernlab")++  kpca_rec <- rec %>%+    step_kpca(X2, X3, X4, X5, X6, id = "")++  kpca_rec$steps[[1]]$keep_original_cols <- NULL++  expect_warning(+    kpca_trained <- prep(kpca_rec, training = tr_dat, verbose = FALSE),+    "'keep_original_cols' was added to"+  )++  expect_error(+    pca_pred <- bake(kpca_trained, new_data = te_dat, all_predictors()),+    NA+  )

ah, apologies, I overlooked the NA here :see_no_evil:

juliasilge

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issue openedr-lib/usethis

Suggestion: add checking on deprecation status to release checklist

I thought it might be helpful if the release checklist created by usethis::use_release_issue() were to include an item about checking on any functions/arguments in different deprecation stages, i.e. the workflow at the end of this section on gradual deprecation?

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un-deprecate `step_kpca()`

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escalate deprecation of `preserve` arg to `step_pls()` and `step_dummy()`

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escalate deprecation of `options` arg to `step_nzv()`

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remove snapshot bc deprecation is undone

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add `step_kpca` back to pkgdown index

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make block for role selection only show up once instead of 4 times

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Merge pull request #802 from tidymodels/deprecation Deprecation clean-up

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pull request commenttidymodels/recipes

export `tidy.check_new_values()`

added them here! closes #809

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update NEWS

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export more tidy methods

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Pull request review commenttidymodels/recipes

Add `keep_original_cols` to `step_kpca()`

 test_that('No kPCA comps', {     tibble::tibble(terms = paste0("X", 2:6), id = "")   ) })+++test_that('keep_original_cols works', {++  skip_if_not_installed("dimRed")+  skip_if_not_installed("kernlab")++  kpca_rec <- rec %>%+    step_kpca(X2, X3, X4, X5, X6, id = "", keep_original_cols = TRUE)++  kpca_trained <- prep(kpca_rec, training = tr_dat, verbose = FALSE)++  pca_pred <- bake(kpca_trained, new_data = te_dat, all_predictors())++  expect_equal(+    colnames(pca_pred),+    c("X2", "X3", "X4", "X5", "X6",+      "kPC1", "kPC2", "kPC3", "kPC4", "kPC5")+  )++})++test_that('can prep recipes with no keep_original_cols', {+  skip_if_not_installed("dimRed")+  skip_if_not_installed("kernlab")++  kpca_rec <- rec %>%+    step_kpca(X2, X3, X4, X5, X6, id = "")++  kpca_rec$steps[[1]]$keep_original_cols <- NULL++  expect_warning(+    kpca_trained <- prep(kpca_rec, training = tr_dat, verbose = FALSE),+    "'keep_original_cols' was added to"+  )++  expect_error(+    pca_pred <- bake(kpca_trained, new_data = te_dat, all_predictors()),+    NA+  )

expect_snapshot() capture the warnings and errors quite nicely, Davis used it several times in his e3 PR

juliasilge

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Pull request review commenttidymodels/recipes

Add `keep_original_cols` to `step_kpca()`

 test_that('No kPCA comps', {     tibble::tibble(terms = paste0("X", 2:6), id = "")   ) })+++test_that('keep_original_cols works', {++  skip_if_not_installed("dimRed")+  skip_if_not_installed("kernlab")++  kpca_rec <- rec %>%+    step_kpca(X2, X3, X4, X5, X6, id = "", keep_original_cols = TRUE)++  kpca_trained <- prep(kpca_rec, training = tr_dat, verbose = FALSE)++  pca_pred <- bake(kpca_trained, new_data = te_dat, all_predictors())++  expect_equal(+    colnames(pca_pred),+    c("X2", "X3", "X4", "X5", "X6",+      "kPC1", "kPC2", "kPC3", "kPC4", "kPC5")+  )++})++test_that('can prep recipes with no keep_original_cols', {+  skip_if_not_installed("dimRed")+  skip_if_not_installed("kernlab")++  kpca_rec <- rec %>%+    step_kpca(X2, X3, X4, X5, X6, id = "")++  kpca_rec$steps[[1]]$keep_original_cols <- NULL++  expect_warning(+    kpca_trained <- prep(kpca_rec, training = tr_dat, verbose = FALSE),+    "'keep_original_cols' was added to"+  )++  expect_error(+    pca_pred <- bake(kpca_trained, new_data = te_dat, all_predictors()),+    NA+  )

Should these be expect_snapshot() now that we have testthat e3?

juliasilge

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issue openedtidymodels/recipes

Export `tidy.check_class()` and `tidy.step_nnmf()`

The tidy methods for the other checks and steps are exported so this seems like an oversight.

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escalate deprecation of `preserve` arg to `step_pls()` and `step_dummy()`

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escalate deprecation of `options` arg to `step_nzv()`

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remove snapshot bc deprecation is undone

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add `step_kpca` back to pkgdown index

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Merge pull request #802 from tidymodels/deprecation Deprecation clean-up

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PR merged tidymodels/recipes

Deprecation clean-up

This PR does a few things with regard to deprecation and sneaks in a bonus clean-up of the pkgdown site:

  • undoes the deprecation of step_kpca(); closes #762
  • escalates the deprecation of the preserve argument to step_pls() and step_dummy()
  • adds lifecycle-style deprecation for the options argument to step_nzv() so it won't get overlooked next time
  • tidies up the pkgdown site so that the newly exported recipes_eval_select() shows up in the section for internal tools rather than at the top and removes the quadruplication of the section on selection via role

The imputation steps and the steps for up/downsampling were already in the correct stage of the deprecation process.

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issue closedtidymodels/recipes

undo deprecation of `step_kpca()`

it was deprecated in version 0.1.7

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hfrick

Pull request review commenttidymodels/dials

class weight parameter for lantern (and other pkgs down the line)

+#' Parameters for class weights for imbalanced problems+#'+#' This parameter can be used to moderate how much influence certain classes+#' receive during training.+#'+#' @inheritParams Laplace+#' @details+#' Used in `lantern::lanter_logistic_reg()` and `lantern::lanter_mlp()`+#' @examples+#' class_weights()+#' @export+class_weights <- function(range = c(1, 10), trans = NULL) {+  new_quant_param(+    type = "double",+    range = range,+    inclusive = c(TRUE, TRUE),+    trans = trans,+    default = 1,+    label = c(class_weights = "Minority Class Weight"),

If the parameter is the weight for a single class, do we want the name to reflect that?

topepo

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Pull request review commenttidymodels/dials

class weight parameter for lantern (and other pkgs down the line)

+#' Parameters for class weights for imbalanced problems+#'+#' This parameter can be used to moderate how much influence certain classes+#' receive during training.+#'+#' @inheritParams Laplace+#' @details+#' Used in `lantern::lanter_logistic_reg()` and `lantern::lanter_mlp()`+#' @examples+#' class_weights()+#' @export+class_weights <- function(range = c(1, 10), trans = NULL) {

do we want a range of [0,1]?

topepo

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pull request commenttidymodels/recipes

Deprecation clean-up

Oh, good catch! Thanks for adding that. :raised_hands:

I've added a single "the" to the sentence and then it cascaded across the standard text width so it looks like a lot more changes than that :eyes:

I think this is ready to be merged. I'll do that once the checks are finished

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issue commenttidymodels/dials

Can't tune recipes::step_window size parameter

Thanks for reporting this @camroberts ! You should now be able to tune both the window and the statistic arguments of step_window() with the development versions of recipes and dials.

camroberts

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delete branch tidymodels/dials

delete branch : summary-stat

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new parameter for rolling summary statistic

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Merge pull request #187 from tidymodels/summary-stat new parameter for summary statistic

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issue closedtidymodels/dials

Can't tune recipes::step_window size parameter

The problem

I'm having trouble with setting up step_window to tune the size parameter. The parameter doesn't seem to be recognized by dials::parameters and the result of tunable looks to be inconsistent. It lists a different parameter name (window instead of size) and the default method in call_info is listed as dials::window instead of dials::window_size.

This looks related to issue #112, but it suggests the problem is isolated to R 4.0 while I'm using R 3.6.3.

For completeness, I also tried to tune the statistic parameter of step_window as it is listed as tunable too. However an error is produced upon creation of the recipe.

Reproducible example

library(tidyverse)
library(tidymodels)
#> Registered S3 method overwritten by 'tune':
#>   method                   from   
#>   required_pkgs.model_spec parsnip

data <- tibble(x = 1:1000,
               y = 3 + .1*x + rnorm(1000))

rec <- recipe(y ~ ., data=data) %>% 
  step_window(x, size=tune())

# The size param is not listed
parameters(rec)
#> Collection of 0 parameters for tuning
#> 
#> [1] identifier type       object    
#> <0 rows> (or 0-length row.names)

# What's tunable?
t <- tunable(rec)
t
#> # A tibble: 2 x 5
#>   name      call_info        source component   component_id
#>   <chr>     <list>           <chr>  <chr>       <chr>       
#> 1 statistic <named list [2]> recipe step_window window_WlPmQ
#> 2 window    <named list [2]> recipe step_window window_WlPmQ

# The "size" arg in step_window is missing. Listed as "window" instead.
# What is the default func?
t$call_info[[2]]
#> $pkg
#> [1] "dials"
#> 
#> $fun
#> [1] "window"
# dials::window doesn't exist. I think it should be dials::window_size.

# tunable says that the "statistic" param is tunable too. But this causes another error:
rec2 <- recipe(y ~ ., data=data) %>% 
  step_window(x, statistic=tune())
#> Error in match(x, table, nomatch = 0L): 'match' requires vector arguments

<sup>Created on 2021-09-01 by the reprex package (v2.0.0)</sup>

<details style="margin-bottom:10px;">

<summary>Session info</summary>

sessioninfo::session_info()
#> - Session info ---------------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.6.3 (2020-02-29)
#>  os       Windows 10 x64              
#>  system   x86_64, mingw32             
#>  ui       RTerm                       
#>  language (EN)                        
#>  collate  English_Australia.1252      
#>  ctype    English_Australia.1252      
#>  tz       Australia/Brisbane          
#>  date     2021-09-01                  
#> 
#> - Packages -------------------------------------------------------------------
#>  package     * version    date       lib source        
#>  assertthat    0.2.1      2019-03-21 [1] CRAN (R 3.6.1)
#>  backports     1.2.1      2020-12-09 [1] CRAN (R 3.6.3)
#>  broom       * 0.7.6      2021-04-05 [1] CRAN (R 3.6.3)
#>  cellranger    1.1.0      2016-07-27 [1] CRAN (R 3.6.1)
#>  class         7.3-18     2021-01-24 [1] CRAN (R 3.6.3)
#>  cli           2.5.0      2021-04-26 [1] CRAN (R 3.6.3)
#>  codetools     0.2-18     2020-11-04 [1] CRAN (R 3.6.3)
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#>  crayon        1.4.1      2021-02-08 [1] CRAN (R 3.6.3)
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#>  dbplyr        2.1.1      2021-04-06 [1] CRAN (R 3.6.3)
#>  dials       * 0.0.9      2020-09-16 [1] CRAN (R 3.6.3)
#>  DiceDesign    1.9        2021-02-13 [1] CRAN (R 3.6.3)
#>  digest        0.6.27     2020-10-24 [1] CRAN (R 3.6.3)
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#>  rlang         0.4.10     2020-12-30 [1] CRAN (R 3.6.3)
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#>  rsample     * 0.1.0      2021-05-08 [1] CRAN (R 3.6.3)
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#>  stringi       1.5.3      2020-09-09 [1] CRAN (R 3.6.3)
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</details>

P.S. Many thanks for the truly fantastic work on tidymodels!

closed time in 16 hours

camroberts

PR merged tidymodels/dials

Reviewers
new parameter for rolling summary statistic

closes #180

a new parameter object for the rolling summary statistic used in recipes::step_window()

@topepo I used summary_stat as the name because that's what was already laid out in the recipes code but am open to a different name if anything has changed since this got put into recipes.

+55 -0

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5 changed files

hfrick

pr closed time in 16 hours

pull request commenttidymodels/recipes

export `tidy.check_new_values()`

While cleaning up the @param tag across tidy methods for various steps and checks I found two more: tidy.check_class() and tidy.step_nnmf() are also not exported. Would it be better to add them here to this PR or make a new one, @DavisVaughan ?

hfrick

comment created time in 16 hours

PR opened tidymodels/recipes

remove `@param x` for steps and checks

closes #806

+6 -87

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80 changed files

pr created time in 16 hours