tidymodels · simonpcouch · Jan 5, 2022 · Nov 10, 2021 · Nov 10, 2021 · Nov 10, 2021
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -23,24 +23,25 @@ jobs:
         config:
           - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: '3.6'}
-          - {os: ubuntu-16.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest", http-user-agent: "R/4.0.0 (ubuntu-16.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: windows-latest, r: 'oldrel-1'}
+          - {os: ubuntu-18.04,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-18.04,   r: 'release'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v1
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
-
-      - uses: r-lib/actions/setup-pandoc@master
+          use-public-rspm: true
 
       - name: Query dependencies
         run: |
@@ -70,6 +71,7 @@ jobs:
           remotes::install_cran("vctrs")
           remotes::install_cran("parsnip")
           remotes::install_cran("tune")
+          remotes::install_cran("kknn")
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -24,16 +24,16 @@ BugReports: https://github.com/tidymodels/stacks/issues
 Depends:
     R (>= 2.10)
 Imports:
-    tune (>= 0.1.2.9000),
+    tune (>= 0.1.3),
     dplyr (>= 1.0.0),
     rlang (>= 0.4.0),
     tibble (>= 2.1.3),
     purrr (>= 0.3.2), 
     parsnip (>= 0.0.4),
     workflows (>= 0.2.2),
     recipes (>= 0.1.15),
-    rsample (>= 0.0.9),
-    workflowsets (>= 0.0.0.9001),
+    rsample (>= 0.1.1),
+    workflowsets (>= 0.1.0),
     butcher (>= 0.1.3),
     yardstick,
     tidyr,
@@ -58,5 +58,5 @@ Suggests:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1.9001
+RoxygenNote: 7.1.2
 VignetteBuilder: knitr
diff --git a/R/collect_parameters.R b/R/collect_parameters.R
@@ -66,7 +66,7 @@ collect_parameters.data_stack <- function(stack, candidates, ...) {
     attributes(stack)$model_metrics,
     candidates,
     attributes(stack)$model_defs,
-    stack
+    stack = stack
   )
 }
 
@@ -79,7 +79,7 @@ collect_parameters.model_stack <- function(stack, candidates, ...) {
     candidates,
     stack$model_defs,
     stack$coefs,
-    stack
+    stack = stack
   )
 }
 

diff --git a/data/class_folds.rda b/data/class_folds.rda
diff --git a/data/class_res_nn.rda b/data/class_res_nn.rda
diff --git a/data/class_res_rf.rda b/data/class_res_rf.rda
diff --git a/data/log_res_nn.rda b/data/log_res_nn.rda
diff --git a/data/log_res_rf.rda b/data/log_res_rf.rda
diff --git a/data/reg_folds.rda b/data/reg_folds.rda
diff --git a/data/reg_res_lr.rda b/data/reg_res_lr.rda
diff --git a/data/reg_res_sp.rda b/data/reg_res_sp.rda
diff --git a/data/reg_res_svm.rda b/data/reg_res_svm.rda
diff --git a/data/tree_frogs_class_test.rda b/data/tree_frogs_class_test.rda
diff --git a/data/tree_frogs_reg_test.rda b/data/tree_frogs_reg_test.rda
diff --git a/man/example_data.Rd b/man/example_data.Rd
diff --git a/man/stacks_description.Rd b/man/stacks_description.Rd
diff --git a/tests/testthat/helper_data.Rda b/tests/testthat/helper_data.Rda
diff --git a/tests/testthat/out/data_stack_class.txt b/tests/testthat/out/data_stack_class.txt
@@ -1,5 +1,5 @@
 > st_class_1
-# A data stack with 1 model definition and 10 candidate members:
-#   class_res_rf: 10 model configurations
+# A data stack with 1 model definition and 9.66666666666667 candidate members:
+#   class_res_rf: 9.66666666666667 model configurations
 # Outcome: reflex (factor)
 
diff --git a/tests/testthat/out/model_stack_class.txt b/tests/testthat/out/model_stack_class.txt
@@ -2,28 +2,24 @@
 Message: -- A stacked ensemble model -------------------------------------
 
 Message: 
-Out of 20 possible candidate members, the ensemble retained 22.
-Penalty: 1e-05.
+Out of 19 possible candidate members, the ensemble retained 6.
+Penalty: 0.1.
 Mixture: 1.
 
-Message: Across the 3 classes, there are an average of 7.33 coefficients per class.
+Message: Across the 3 classes, there are an average of 3 coefficients per class.
 
 Message: 
-The 10 highest weighted member classes are:
+The 6 highest weighted member classes are:
 
-# A tibble: 10 x 4
-   member                       type        weight class
-   <chr>                        <chr>        <dbl> <chr>
- 1 .pred_mid_class_res_rf_1_04  rand_forest   39.8 low  
- 2 .pred_mid_class_res_rf_1_06  rand_forest   35.3 mid  
- 3 .pred_mid_class_res_rf_1_09  rand_forest   23.5 mid  
- 4 .pred_full_class_res_rf_1_05 rand_forest   21.7 full 
- 5 .pred_full_class_res_rf_1_04 rand_forest   17.0 low  
- 6 .pred_full_class_res_rf_1_09 rand_forest   16.6 mid  
- 7 .pred_mid_class_res_rf_1_02  rand_forest   13.3 low  
- 8 .pred_mid_class_res_rf_1_01  rand_forest   13.3 mid  
- 9 .pred_mid_class_res_rf_1_10  rand_forest   11.9 low  
-10 .pred_mid_class_res_rf_1_03  rand_forest   11.4 low  
+# A tibble: 6 x 4
+  member                       type        weight class
+  <chr>                        <chr>        <dbl> <chr>
+1 .pred_full_class_res_rf_1_05 rand_forest 3.75   full 
+2 .pred_mid_class_res_rf_1_06  rand_forest 0.674  mid  
+3 .pred_full_class_res_rf_1_07 rand_forest 0.411  full 
+4 .pred_full_class_res_rf_1_01 rand_forest 0.0957 full 
+5 .pred_full_class_res_rf_1_06 rand_forest 0.0193 full 
+6 .pred_full_class_res_rf_1_04 rand_forest 0.0110 full 
 
 Message: 
 Members have not yet been fitted with `fit_members()`.

diff --git a/tests/testthat/out/model_stack_class_fit.txt b/tests/testthat/out/model_stack_class_fit.txt
@@ -2,26 +2,22 @@
 Message: -- A stacked ensemble model -------------------------------------
 
 Message: 
-Out of 20 possible candidate members, the ensemble retained 22.
-Penalty: 1e-05.
+Out of 19 possible candidate members, the ensemble retained 6.
+Penalty: 0.1.
 Mixture: 1.
 
-Message: Across the 3 classes, there are an average of 7.33 coefficients per class.
+Message: Across the 3 classes, there are an average of 3 coefficients per class.
 
 Message: 
-The 10 highest weighted member classes are:
+The 6 highest weighted member classes are:
 
-# A tibble: 10 x 4
-   member                       type        weight class
-   <chr>                        <chr>        <dbl> <chr>
- 1 .pred_mid_class_res_rf_1_04  rand_forest   39.8 low  
- 2 .pred_mid_class_res_rf_1_06  rand_forest   35.3 mid  
- 3 .pred_mid_class_res_rf_1_09  rand_forest   23.5 mid  
- 4 .pred_full_class_res_rf_1_05 rand_forest   21.7 full 
- 5 .pred_full_class_res_rf_1_04 rand_forest   17.0 low  
- 6 .pred_full_class_res_rf_1_09 rand_forest   16.6 mid  
- 7 .pred_mid_class_res_rf_1_02  rand_forest   13.3 low  
- 8 .pred_mid_class_res_rf_1_01  rand_forest   13.3 mid  
- 9 .pred_mid_class_res_rf_1_10  rand_forest   11.9 low  
-10 .pred_mid_class_res_rf_1_03  rand_forest   11.4 low  
+# A tibble: 6 x 4
+  member                       type        weight class
+  <chr>                        <chr>        <dbl> <chr>
+1 .pred_full_class_res_rf_1_05 rand_forest 3.75   full 
+2 .pred_mid_class_res_rf_1_06  rand_forest 0.674  mid  
+3 .pred_full_class_res_rf_1_07 rand_forest 0.411  full 
+4 .pred_full_class_res_rf_1_01 rand_forest 0.0957 full 
+5 .pred_full_class_res_rf_1_06 rand_forest 0.0193 full 
+6 .pred_full_class_res_rf_1_04 rand_forest 0.0110 full 
 
diff --git a/tests/testthat/out/model_stack_log.txt b/tests/testthat/out/model_stack_log.txt
@@ -2,18 +2,19 @@
 Message: -- A stacked ensemble model -------------------------------------
 
 Message: 
-Out of 10 possible candidate members, the ensemble retained 2.
-Penalty: 0.1.
+Out of 10 possible candidate members, the ensemble retained 3.
+Penalty: 1e-05.
 Mixture: 1.
 
 Message: 
-The 2 highest weighted member classes are:
+The 3 highest weighted member classes are:
 
-# A tibble: 2 x 3
+# A tibble: 3 x 3
   member                    type        weight
   <chr>                     <chr>        <dbl>
-1 .pred_yes_log_res_rf_1_03 rand_forest 3.54  
-2 .pred_yes_log_res_rf_1_06 rand_forest 0.0457
+1 .pred_yes_log_res_rf_1_05 rand_forest  3.56 
+2 .pred_yes_log_res_rf_1_02 rand_forest  3.22 
+3 .pred_yes_log_res_rf_1_09 rand_forest  0.226
 
 Message: 
 Members have not yet been fitted with `fit_members()`.

diff --git a/tests/testthat/out/model_stack_log_fit.txt b/tests/testthat/out/model_stack_log_fit.txt
@@ -2,16 +2,17 @@
 Message: -- A stacked ensemble model -------------------------------------
 
 Message: 
-Out of 10 possible candidate members, the ensemble retained 2.
-Penalty: 0.1.
+Out of 10 possible candidate members, the ensemble retained 3.
+Penalty: 1e-05.
 Mixture: 1.
 
 Message: 
-The 2 highest weighted member classes are:
+The 3 highest weighted member classes are:
 
-# A tibble: 2 x 3
+# A tibble: 3 x 3
   member                    type        weight
   <chr>                     <chr>        <dbl>
-1 .pred_yes_log_res_rf_1_03 rand_forest 3.54  
-2 .pred_yes_log_res_rf_1_06 rand_forest 0.0457
+1 .pred_yes_log_res_rf_1_05 rand_forest  3.56 
+2 .pred_yes_log_res_rf_1_02 rand_forest  3.22 
+3 .pred_yes_log_res_rf_1_09 rand_forest  0.226
 
diff --git a/tests/testthat/out/model_stack_reg.txt b/tests/testthat/out/model_stack_reg.txt
@@ -2,19 +2,18 @@
 Message: -- A stacked ensemble model -------------------------------------
 
 Message: 
-Out of 5 possible candidate members, the ensemble retained 3.
+Out of 5 possible candidate members, the ensemble retained 2.
 Penalty: 0.1.
 Mixture: 1.
 
 Message: 
-The 3 highest weighted members are:
+The 2 highest weighted members are:
 
-# A tibble: 3 x 3
+# A tibble: 2 x 3
   member          type    weight
   <chr>           <chr>    <dbl>
-1 reg_res_svm_1_5 svm_rbf  2.88 
-2 reg_res_svm_1_3 svm_rbf  0.895
-3 reg_res_svm_1_1 svm_rbf  0.410
+1 reg_res_svm_1_3 svm_rbf  1.26 
+2 reg_res_svm_1_2 svm_rbf  0.136
 
 Message: 
 Members have not yet been fitted with `fit_members()`.

diff --git a/tests/testthat/out/model_stack_reg_fit.txt b/tests/testthat/out/model_stack_reg_fit.txt
@@ -2,17 +2,16 @@
 Message: -- A stacked ensemble model -------------------------------------
 
 Message: 
-Out of 5 possible candidate members, the ensemble retained 3.
+Out of 5 possible candidate members, the ensemble retained 2.
 Penalty: 0.1.
 Mixture: 1.
 
 Message: 
-The 3 highest weighted members are:
+The 2 highest weighted members are:
 
-# A tibble: 3 x 3
+# A tibble: 2 x 3
   member          type    weight
   <chr>           <chr>    <dbl>
-1 reg_res_svm_1_5 svm_rbf  2.88 
-2 reg_res_svm_1_3 svm_rbf  0.895
-3 reg_res_svm_1_1 svm_rbf  0.410
+1 reg_res_svm_1_3 svm_rbf  1.26 
+2 reg_res_svm_1_2 svm_rbf  0.136
 
diff --git a/tests/testthat/test_collect_parameters.R b/tests/testthat/test_collect_parameters.R
@@ -55,7 +55,7 @@ test_that("collect_parameters on a data stack works (regression)", {
   expect_equal(nrow(res), 5)
 
   expect_equal(ncol(res2), 2)
-  expect_equal(nrow(res2), 9)
+  expect_equal(nrow(res2), 10)
 
   expect_equal(ncol(res3), 1)
   expect_equal(nrow(res3), 1)
@@ -73,7 +73,7 @@ test_that("collect_parameters on a model stack works (regression)", {
   expect_equal(nrow(res), 5)
 
   expect_equal(ncol(res2), 3)
-  expect_equal(nrow(res2), 9)
+  expect_equal(nrow(res2), 10)
 
   expect_true(
     all(
@@ -100,5 +100,5 @@ test_that("collect_parameters works (classification)", {
   expect_equal(nrow(res), 10)
 
   expect_equal(ncol(res2), 6)
-  expect_equal(nrow(res2), 60)
+  expect_equal(nrow(res2), 57)
 })