From b33b0d3d061fb5d0942caaf450e4473000fba4b2 Mon Sep 17 00:00:00 2001
From: James Wade <jhwade@dow.com>
Date: Fri, 2 Feb 2024 10:11:28 -0500
Subject: [PATCH 01/11] update snapshots

---
 tests/testthat/_snaps/measure_input_long.md  | 12 ++---
 tests/testthat/_snaps/measure_input_wide.md  |  6 +--
 tests/testthat/_snaps/measure_output_long.md |  4 +-
 tests/testthat/_snaps/measure_output_wide.md |  4 +-
 tests/testthat/_snaps/savitzky_golay.md      | 48 ++++++++++----------
 tests/testthat/helpers-data.R                | 16 +++----
 6 files changed, 45 insertions(+), 45 deletions(-)

diff --git a/tests/testthat/_snaps/measure_input_long.md b/tests/testthat/_snaps/measure_input_long.md
index 3e1f939..e115358 100644
--- a/tests/testthat/_snaps/measure_input_long.md
+++ b/tests/testthat/_snaps/measure_input_long.md
@@ -2,7 +2,7 @@
 
     Code
       print(rec_1)
-    Message <cliMessage>
+    Message
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -43,7 +43,7 @@
 
     Code
       print(prep_1)
-    Message <cliMessage>
+    Message
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -87,7 +87,7 @@
     Code
       recipe(water + fat + protein ~ absorp, data = na_train) %>%
         step_measure_input_long(absorp) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_input_long()`:
       Caused by error in `prep()`:
       ! 'location' is required for long input data
@@ -97,7 +97,7 @@
     Code
       recipe(water + fat + protein ~ ., data = miss_train) %>%
         step_measure_input_long(absorp, location = vars(ind)) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_input_long()`:
       Caused by error in `check_measure_dims()`:
       ! The number of rows in each measure should be the same. Most samples have 100 rows and these do not: 1. Please pad the input with missing values.
@@ -107,7 +107,7 @@
     Code
       recipe(water + fat + protein ~ ., data = na_train) %>% step_measure_input_long(
         dplyr::everything(), location = vars(ind)) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_input_long()`:
       Caused by error in `check_single_selector()`:
       ! The selection for `...` should only select a single column (6 columns were selected).
@@ -117,7 +117,7 @@
     Code
       recipe(water + fat + protein ~ ., data = na_train) %>% step_measure_input_long(
         absorp, location = vars(dplyr::everything())) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_input_long()`:
       Caused by error in `check_single_selector()`:
       ! The selection for `location` should only select a single column (6 columns were selected).
diff --git a/tests/testthat/_snaps/measure_input_wide.md b/tests/testthat/_snaps/measure_input_wide.md
index 5c84336..98d5e98 100644
--- a/tests/testthat/_snaps/measure_input_wide.md
+++ b/tests/testthat/_snaps/measure_input_wide.md
@@ -2,7 +2,7 @@
 
     Code
       print(rec_1)
-    Message <cliMessage>
+    Message
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -48,7 +48,7 @@
 
     Code
       print(prep_1)
-    Message <cliMessage>
+    Message
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -92,7 +92,7 @@
     Code
       recipe(water + fat + protein ~ ., data = na_train) %>% step_measure_input_wide(
         x_001:x_100, location_values = 1:2) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_input_wide()`:
       Caused by error in `prep()`:
       ! 100 columns were selected as inputs but `location_values` has 2 values.
diff --git a/tests/testthat/_snaps/measure_output_long.md b/tests/testthat/_snaps/measure_output_long.md
index 639e464..a278c4e 100644
--- a/tests/testthat/_snaps/measure_output_long.md
+++ b/tests/testthat/_snaps/measure_output_long.md
@@ -2,7 +2,7 @@
 
     Code
       print(rec_1)
-    Message <cliMessage>
+    Message
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -45,7 +45,7 @@
 
     Code
       print(prep_1)
-    Message <cliMessage>
+    Message
       
       -- Recipe ----------------------------------------------------------------------
       
diff --git a/tests/testthat/_snaps/measure_output_wide.md b/tests/testthat/_snaps/measure_output_wide.md
index eb6c68c..c6d6f84 100644
--- a/tests/testthat/_snaps/measure_output_wide.md
+++ b/tests/testthat/_snaps/measure_output_wide.md
@@ -2,7 +2,7 @@
 
     Code
       print(rec_1)
-    Message <cliMessage>
+    Message
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -45,7 +45,7 @@
 
     Code
       print(prep_1)
-    Message <cliMessage>
+    Message
       
       -- Recipe ----------------------------------------------------------------------
       
diff --git a/tests/testthat/_snaps/savitzky_golay.md b/tests/testthat/_snaps/savitzky_golay.md
index cf647a4..b664c7c 100644
--- a/tests/testthat/_snaps/savitzky_golay.md
+++ b/tests/testthat/_snaps/savitzky_golay.md
@@ -47,7 +47,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -57,7 +57,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -67,7 +67,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -77,7 +77,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -87,7 +87,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -97,7 +97,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -107,7 +107,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -117,7 +117,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -127,7 +127,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -137,7 +137,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -147,7 +147,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -157,7 +157,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -167,7 +167,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -177,7 +177,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -187,7 +187,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -197,7 +197,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -207,7 +207,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -217,7 +217,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -227,7 +227,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -237,7 +237,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -247,7 +247,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -257,7 +257,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -267,7 +267,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -277,7 +277,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Error <recipes_error_step>
+    Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
diff --git a/tests/testthat/helpers-data.R b/tests/testthat/helpers-data.R
index 4aabead..69c1c6f 100644
--- a/tests/testthat/helpers-data.R
+++ b/tests/testthat/helpers-data.R
@@ -11,20 +11,20 @@ data_meat_long <- function() {
   meats_2 <-
     meats %>%
     mutate(.sample_num = row_number()) %>%
-    tidyr::pivot_longer(
+    pivot_longer(
       cols = c(x_001:x_100),
       names_to = "temp",
       values_to = "absorp"
     ) %>%
-    dplyr::full_join(inds, by = "temp") %>%
-    dplyr:: select(-temp)
+    full_join(inds, by = "temp") %>%
+    select(-temp)
 
   inds <- tibble(temp = grep("^x_", names(meats), value = TRUE),
                  ind = seq(1, 17, length.out = 100))
 
   list(
-    train = meats_2 %>% dplyr::filter(.sample_num <= 200),
-    test  = meats_2 %>% dplyr::filter(.sample_num >  200)
+    train = meats_2 %>% filter(.sample_num <= 200),
+    test  = meats_2 %>% filter(.sample_num >  200)
     )
 }
 
@@ -38,11 +38,11 @@ data_meat_wide <- function() {
   meats_2 <-
     meats %>%
     mutate(.sample_num = row_number()) %>%
-    dplyr::relocate(.sample_num)
+    relocate(.sample_num)
 
   list(
-    train = meats_2 %>% dplyr::filter(.sample_num <= 200),
-    test  = meats_2 %>% dplyr::filter(.sample_num >  200),
+    train = meats_2 %>% filter(.sample_num <= 200),
+    test  = meats_2 %>% filter(.sample_num >  200),
     ind = seq(1, 17, length.out = 100)
   )
 }

From 9d88ce3ab291b288feb3c6b8e54830d445d93893 Mon Sep 17 00:00:00 2001
From: James Wade <jhwade@dow.com>
Date: Fri, 2 Feb 2024 10:12:56 -0500
Subject: [PATCH 02/11] update roxygen

---
 DESCRIPTION                   |  2 +-
 tests/testthat/helpers-data.R | 51 -----------------------------------
 2 files changed, 1 insertion(+), 52 deletions(-)
 delete mode 100644 tests/testthat/helpers-data.R

diff --git a/DESCRIPTION b/DESCRIPTION
index fc96346..c1f5de7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -39,4 +39,4 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3.9000
+RoxygenNote: 7.3.1
diff --git a/tests/testthat/helpers-data.R b/tests/testthat/helpers-data.R
deleted file mode 100644
index 69c1c6f..0000000
--- a/tests/testthat/helpers-data.R
+++ /dev/null
@@ -1,51 +0,0 @@
-data_meat_long <- function() {
-  skip_if_not_installed("modeldata")
-  data(meats, package = "modeldata")
-
-  library(tidyr)
-  library(dplyr)
-
-  inds <- tibble(temp = grep("^x_", names(meats), value = TRUE),
-                 ind = seq(1, 17, length.out = 100))
-
-  meats_2 <-
-    meats %>%
-    mutate(.sample_num = row_number()) %>%
-    pivot_longer(
-      cols = c(x_001:x_100),
-      names_to = "temp",
-      values_to = "absorp"
-    ) %>%
-    full_join(inds, by = "temp") %>%
-    select(-temp)
-
-  inds <- tibble(temp = grep("^x_", names(meats), value = TRUE),
-                 ind = seq(1, 17, length.out = 100))
-
-  list(
-    train = meats_2 %>% filter(.sample_num <= 200),
-    test  = meats_2 %>% filter(.sample_num >  200)
-    )
-}
-
-data_meat_wide <- function() {
-  skip_if_not_installed("modeldata")
-  data(meats, package = "modeldata")
-
-  library(tidyr)
-  library(dplyr)
-
-  meats_2 <-
-    meats %>%
-    mutate(.sample_num = row_number()) %>%
-    relocate(.sample_num)
-
-  list(
-    train = meats_2 %>% filter(.sample_num <= 200),
-    test  = meats_2 %>% filter(.sample_num >  200),
-    ind = seq(1, 17, length.out = 100)
-  )
-}
-
-
-

From c6b36b4c007f2abbeae100afe638231e11e41369 Mon Sep 17 00:00:00 2001
From: James Wade <jhwade@dow.com>
Date: Fri, 2 Feb 2024 10:13:23 -0500
Subject: [PATCH 03/11] chore: remove explicity namespace

---
 tests/testthat/helpers-data.R | 51 +++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 tests/testthat/helpers-data.R

diff --git a/tests/testthat/helpers-data.R b/tests/testthat/helpers-data.R
new file mode 100644
index 0000000..69c1c6f
--- /dev/null
+++ b/tests/testthat/helpers-data.R
@@ -0,0 +1,51 @@
+data_meat_long <- function() {
+  skip_if_not_installed("modeldata")
+  data(meats, package = "modeldata")
+
+  library(tidyr)
+  library(dplyr)
+
+  inds <- tibble(temp = grep("^x_", names(meats), value = TRUE),
+                 ind = seq(1, 17, length.out = 100))
+
+  meats_2 <-
+    meats %>%
+    mutate(.sample_num = row_number()) %>%
+    pivot_longer(
+      cols = c(x_001:x_100),
+      names_to = "temp",
+      values_to = "absorp"
+    ) %>%
+    full_join(inds, by = "temp") %>%
+    select(-temp)
+
+  inds <- tibble(temp = grep("^x_", names(meats), value = TRUE),
+                 ind = seq(1, 17, length.out = 100))
+
+  list(
+    train = meats_2 %>% filter(.sample_num <= 200),
+    test  = meats_2 %>% filter(.sample_num >  200)
+    )
+}
+
+data_meat_wide <- function() {
+  skip_if_not_installed("modeldata")
+  data(meats, package = "modeldata")
+
+  library(tidyr)
+  library(dplyr)
+
+  meats_2 <-
+    meats %>%
+    mutate(.sample_num = row_number()) %>%
+    relocate(.sample_num)
+
+  list(
+    train = meats_2 %>% filter(.sample_num <= 200),
+    test  = meats_2 %>% filter(.sample_num >  200),
+    ind = seq(1, 17, length.out = 100)
+  )
+}
+
+
+

From dfb917b564a61826ef43269ce0b2b6e75efc8a1f Mon Sep 17 00:00:00 2001
From: James Wade <jhwade@dow.com>
Date: Fri, 2 Feb 2024 10:38:04 -0500
Subject: [PATCH 04/11] remove unused na_rm arg

---
 R/input_long.R | 2 +-
 R/input_wide.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/input_long.R b/R/input_long.R
index cf1b354..5135f41 100644
--- a/R/input_long.R
+++ b/R/input_long.R
@@ -71,7 +71,7 @@ step_measure_input_long <-
   }
 
 step_measure_input_long_new <-
-  function(terms, role, trained, columns, location, na_rm, skip, id) {
+  function(terms, role, trained, columns, location, skip, id) {
     step(
       subclass = "measure_input_long",
       terms = terms,
diff --git a/R/input_wide.R b/R/input_wide.R
index 3ee49a0..1246029 100644
--- a/R/input_wide.R
+++ b/R/input_wide.R
@@ -89,7 +89,7 @@ step_measure_input_wide <-
     }
 
 step_measure_input_wide_new <-
-  function(terms, role, trained, columns, location_values, na_rm, skip, id) {
+  function(terms, role, trained, columns, location_values, skip, id) {
     step(
       subclass = "measure_input_wide",
       terms = terms,

From 4f7c912b6b887fb6a8704b6fd94b16484663b042 Mon Sep 17 00:00:00 2001
From: James Wade <jhwade@dow.com>
Date: Fri, 2 Feb 2024 10:38:15 -0500
Subject: [PATCH 05/11] change filename

---
 R/{meats.R => data-meats.R} | 0
 man/meats_long.Rd           | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename R/{meats.R => data-meats.R} (100%)

diff --git a/R/meats.R b/R/data-meats.R
similarity index 100%
rename from R/meats.R
rename to R/data-meats.R
diff --git a/man/meats_long.Rd b/man/meats_long.Rd
index a0cbec3..7b0ea81 100644
--- a/man/meats_long.Rd
+++ b/man/meats_long.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/meats.R
+% Please edit documentation in R/data-meats.R
 \docType{data}
 \name{meats_long}
 \alias{meats_long}

From 65b511efb4d90ef0bacbbca974eb2d637ecd193b Mon Sep 17 00:00:00 2001
From: James Wade <jhwade@dow.com>
Date: Fri, 2 Feb 2024 10:42:39 -0500
Subject: [PATCH 06/11] ci: update workflows

---
 .github/workflows/R-CMD-check.yaml   | 15 +--------------
 .github/workflows/pr-commands.yaml   |  4 ++--
 .github/workflows/test-coverage.yaml |  6 +++---
 3 files changed, 6 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index ee65ccb..74d8c97 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -1,9 +1,5 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
-#
-# NOTE: This workflow is overkill for most R packages and
-# check-standard.yaml is likely a better choice.
-# usethis::use_github_action("check-standard") will install it.
 on:
   push:
     branches: [main, master]
@@ -23,26 +19,17 @@ jobs:
       matrix:
         config:
           - {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'}
-
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
-          - {os: ubuntu-latest,   r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
index 71f335b..eea58c5 100644
--- a/.github/workflows/pr-commands.yaml
+++ b/.github/workflows/pr-commands.yaml
@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -51,7 +51,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 2c5bb50..960234c 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -31,7 +31,7 @@ jobs:
           covr::codecov(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
         shell: Rscript {0}
 
@@ -44,7 +44,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

From 8a2d31ae258a4c0d25f599b20fe3d055f7d7bc6c Mon Sep 17 00:00:00 2001
From: James Wade <jhwade@dow.com>
Date: Fri, 2 Feb 2024 14:00:12 -0500
Subject: [PATCH 07/11] feat: measures padding helper function for missing data

---
 R/checks.R | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/R/checks.R b/R/checks.R
index 97f4e4c..e9e95d3 100644
--- a/R/checks.R
+++ b/R/checks.R
@@ -31,3 +31,30 @@ check_measure_dims <- function(x) {
   }
   invisible(NULL)
 }
+
+pad_measure_dims <- function(x) {
+  # Determine the most frequent number of rows
+  num_rows <- purrr::map_int(x$.measures, nrow)
+  num_unique <- sort(table(num_rows), decreasing = TRUE)
+  most_freq <- as.integer(names(num_unique)[1])
+
+  # Pad each measure so they all have 'most_freq' rows
+  x$.measures <- purrr::map(x$.measures, ~{
+    df <- .x
+    if (nrow(df) < most_freq) {
+      # Calculate how many rows to add
+      rows_to_add <- most_freq - nrow(df)
+      # Create a data frame with the required number of missing rows
+      missing_rows <-
+        purrr::map_dfc(names(df), ~rep(NA_real_, rows_to_add)) %>%
+        tibble::as_tibble() %>%
+        setNames(names(df)) %>%
+        suppressMessages() # suppress message about new column names
+      # Bind the missing rows to the original data frame
+      df <- bind_rows(df, missing_rows)
+      df
+    }
+    df
+  })
+  x
+}

From e576acc62d420644876dacdc70268719789490db Mon Sep 17 00:00:00 2001
From: James Wade <jhwade@dow.com>
Date: Fri, 2 Feb 2024 14:01:24 -0500
Subject: [PATCH 08/11] feat: add pad argument to input_long and remove NA
 'values' from output_wide

---
 R/input_long.R                 | 24 +++++++++++++++++-------
 R/output_wide.R                |  2 ++
 man/step_measure_input_long.Rd |  9 +++++++--
 3 files changed, 26 insertions(+), 9 deletions(-)

diff --git a/R/input_long.R b/R/input_long.R
index 5135f41..d7cd715 100644
--- a/R/input_long.R
+++ b/R/input_long.R
@@ -7,14 +7,16 @@
 #' @family input/output steps
 #' @inheritParams recipes::step_center
 #' @param ... One or more selector functions to choose which _single_ column
-#' contains the analytical measurements. The selection should be in the order
-#' of the measurement's profile.
+#'   contains the analytical measurements. The selection should be in the order
+#'   of the measurement's profile.
 #' @param location One or more selector functions to choose which _single_
-#' column has the locations of the analytical values.
+#'   column has the locations of the analytical values.
+#' @param pad Whether to pad the measurements to ensure that they all have the
+#'   same number of values. This is useful when there are missing values in the
+#'   measurements.
 #' @param columns A character vector of column names determined by the recipe.
-#' @details
-#' This step is designed for data in a format where there is a column for the
-#' analytical measurement (e.g., absorption, etc.) and another with the
+#' @details This step is designed for data in a format where there is a column
+#' for the analytical measurement (e.g., absorption, etc.) and another with the
 #' location of the value (e.g., wave number, etc.).
 #'
 #' `step_measure_input_long()` will collect those data and put them into a
@@ -48,6 +50,7 @@ step_measure_input_long <-
   function(recipe,
            ...,
            location,
+           pad = FALSE,
            role = "measure",
            trained = FALSE,
            columns = NULL,
@@ -64,6 +67,7 @@ step_measure_input_long <-
         role = role,
         columns = columns,
         location = location,
+        pad = pad,
         skip = skip,
         id = id
       )
@@ -71,7 +75,7 @@ step_measure_input_long <-
   }
 
 step_measure_input_long_new <-
-  function(terms, role, trained, columns, location, skip, id) {
+  function(terms, role, trained, columns, location, pad, skip, id) {
     step(
       subclass = "measure_input_long",
       terms = terms,
@@ -79,6 +83,7 @@ step_measure_input_long_new <-
       trained = trained,
       columns = columns,
       location = location,
+      pad = pad,
       skip = skip,
       id = id
     )
@@ -104,6 +109,7 @@ prep.step_measure_input_long <- function(x, training, info = NULL, ...) {
     trained = TRUE,
     columns = unname(c(value_name, loc_name)),
     location = x$location,
+    pad = x$pad,
     skip = x$skip,
     id = x$id
   )
@@ -125,6 +131,10 @@ bake.step_measure_input_long <- function(object, new_data, ...) {
       tidyr::nest(.by = c(-value), .key = ".measures")
   }
 
+  if (rlang::is_true(object$pad)) {
+    new_data <- pad_measure_dims(new_data)
+  }
+
   check_measure_dims(new_data)
 
   new_data
diff --git a/R/output_wide.R b/R/output_wide.R
index 178d9f6..c5f022e 100644
--- a/R/output_wide.R
+++ b/R/output_wide.R
@@ -95,6 +95,8 @@ bake.step_measure_output_wide <- function(object, new_data, ...) {
     new_data %>%
     tidyr::unnest(cols = c(.measures)) %>%
     dplyr::mutate(location = gsub(" ", "0", format(location))) %>%
+    # remove NA values that are introduced by padding
+    tidyr::drop_na("value") %>%
     tidyr::pivot_wider(
       id_cols = c(dplyr::all_of(non_meas)),
       names_from = "location",
diff --git a/man/step_measure_input_long.Rd b/man/step_measure_input_long.Rd
index 7f38f6a..ee77f4e 100644
--- a/man/step_measure_input_long.Rd
+++ b/man/step_measure_input_long.Rd
@@ -8,6 +8,7 @@ step_measure_input_long(
   recipe,
   ...,
   location,
+  pad = FALSE,
   role = "measure",
   trained = FALSE,
   columns = NULL,
@@ -26,6 +27,10 @@ of the measurement's profile.}
 \item{location}{One or more selector functions to choose which \emph{single}
 column has the locations of the analytical values.}
 
+\item{pad}{Whether to pad the measurements to ensure that they all have the
+same number of values. This is useful when there are missing values in the
+measurements.}
+
 \item{role}{Not used by this step since no new variables are
 created.}
 
@@ -50,8 +55,8 @@ step that converts measures organized in a column for the analytical results
 the package.
 }
 \details{
-This step is designed for data in a format where there is a column for the
-analytical measurement (e.g., absorption, etc.) and another with the
+This step is designed for data in a format where there is a column
+for the analytical measurement (e.g., absorption, etc.) and another with the
 location of the value (e.g., wave number, etc.).
 
 \code{step_measure_input_long()} will collect those data and put them into a

From 3f691192ad36ce25f25b2ca10d2f98edc1ed696f Mon Sep 17 00:00:00 2001
From: James Wade <jhwade@dow.com>
Date: Fri, 2 Feb 2024 14:03:41 -0500
Subject: [PATCH 09/11] [test] add padding to tests and update snapshots

---
 tests/testthat/_snaps/measure_output_long.md | 16 ++++++++++++++++
 tests/testthat/_snaps/measure_output_wide.md | 14 ++++++++++++++
 tests/testthat/test_measure_output_long.R    | 16 +++++++++++++---
 tests/testthat/test_measure_output_wide.R    | 13 ++++++++++++-
 4 files changed, 55 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/_snaps/measure_output_long.md b/tests/testthat/_snaps/measure_output_long.md
index a278c4e..c5acf98 100644
--- a/tests/testthat/_snaps/measure_output_long.md
+++ b/tests/testthat/_snaps/measure_output_long.md
@@ -88,3 +88,19 @@
       1      1 step      measure_input_long  TRUE    FALSE potato
       2      2 step      measure_output_long TRUE    FALSE turnip
 
+---
+
+    Error in `step_measure_input_long()`:
+    Caused by error in `check_measure_dims()`:
+    ! The number of rows in each measure should be the same. Most samples have 2 rows and these do not: 1. Please pad the input with missing values.
+
+---
+
+    Code
+      recipe(water + fat + protein ~ ., data = meats_train) %>%
+        step_measure_output_long() %>% prep()
+    Condition
+      Error in `step_measure_output_long()`:
+      Caused by error in `check_has_measure()`:
+      ! It appears that the measurements have not been converted for the inernal format. See `step_measure_input_long()` and `step_measure_input_wide()` and use these prior to `step_measure_output_long()`.
+
diff --git a/tests/testthat/_snaps/measure_output_wide.md b/tests/testthat/_snaps/measure_output_wide.md
index c6d6f84..314d1a9 100644
--- a/tests/testthat/_snaps/measure_output_wide.md
+++ b/tests/testthat/_snaps/measure_output_wide.md
@@ -88,3 +88,17 @@
       1      1 step      measure_input_long  TRUE    FALSE potato
       2      2 step      measure_output_wide TRUE    FALSE turnip
 
+---
+
+    object 'miss_train_padded' not found
+
+---
+
+    Code
+      recipe(water + fat + protein ~ ., data = meats_train) %>%
+        step_measure_output_wide() %>% prep()
+    Condition
+      Error in `step_measure_output_wide()`:
+      Caused by error in `check_has_measure()`:
+      ! It appears that the measurements have not been converted for the inernal format. See `step_measure_input_long()` and `step_measure_input_wide()` and use these prior to `step_measure_output_wide()`.
+
diff --git a/tests/testthat/test_measure_output_long.R b/tests/testthat/test_measure_output_long.R
index 4e525d9..c464712 100644
--- a/tests/testthat/test_measure_output_long.R
+++ b/tests/testthat/test_measure_output_long.R
@@ -45,12 +45,22 @@ test_that("output long format data", {
 
   ### missing rows
 
-  bake_2 <-
+  expect_snapshot_error(
     recipe(water + fat + protein ~ ., data = miss_train) %>%
-    step_measure_input_long(absorp, location = vars(ind)) %>%
+      step_measure_input_long(absorp, location = vars(ind)) %>%
+      step_measure_output_long("rstudio", "posit", id = "turnip") %>%
+      prep() %>%
+      bake(new_data = NULL)
+  )
+
+  ### missing rows with padding
+
+  bake_2 <- recipe(water + fat + protein ~ ., data = miss_train) %>%
+    step_measure_input_long(absorp, location = vars(ind), pad = TRUE) %>%
     step_measure_output_long("rstudio", "posit", id = "turnip") %>%
     prep() %>%
     bake(new_data = NULL)
+
   dat_ptype <-
     tibble::tibble(
       .sample_num = integer(0),
@@ -61,7 +71,7 @@ test_that("output long format data", {
       posit = numeric(0)
     )
   expect_equal(bake_2[0,], dat_ptype)
-  expect_equal(nrow(bake_2), 399L)
+  expect_equal(nrow(bake_2), 400L)
 
   ## missing values
 
diff --git a/tests/testthat/test_measure_output_wide.R b/tests/testthat/test_measure_output_wide.R
index c4967d6..2754cb2 100644
--- a/tests/testthat/test_measure_output_wide.R
+++ b/tests/testthat/test_measure_output_wide.R
@@ -45,12 +45,23 @@ test_that("output wide format data", {
 
   ### missing rows
 
+  expect_snapshot_error(
+    recipe(water + fat + protein ~ ., data = miss_train_padded) %>%
+      step_measure_input_long(absorp, location = vars(ind)) %>%
+      step_measure_output_wide(id = "turnip") %>%
+      prep() %>%
+      bake(new_data = NULL)
+  )
+
+  ### missing rows with padding
+
   bake_2 <-
     recipe(water + fat + protein ~ ., data = miss_train) %>%
-    step_measure_input_long(absorp, location = vars(ind)) %>%
+    step_measure_input_long(absorp, location = vars(ind), pad = TRUE) %>%
     step_measure_output_wide(id = "turnip") %>%
     prep() %>%
     bake(new_data = NULL)
+  # one NA value from padding takes complete cases from 200L -> 199L
   expect_equal(sum(complete.cases(bake_2)), 199L)
   expect_true(is.na(bake_2$measure_1.161616[1]))
 

From 20ca58760330878d10eef300976e92a96c865eb1 Mon Sep 17 00:00:00 2001
From: James Wade <jhwade@dow.com>
Date: Fri, 2 Feb 2024 14:38:19 -0500
Subject: [PATCH 10/11] [chore] styler

---
 R/baseline.R                               |  13 +--
 R/checks.R                                 |  10 +-
 R/helpers.R                                |  12 ++-
 R/input_long.R                             |  14 +--
 R/input_wide.R                             |  59 ++++++-----
 R/output_long.R                            |  26 +++--
 R/output_wide.R                            |  20 ++--
 R/savitzky_golay.R                         |  77 +++++++-------
 tests/testthat/helpers-data.R              |  21 ++--
 tests/testthat/test-data-transformations.R |   6 --
 tests/testthat/test_measure_input_long.R   |   8 +-
 tests/testthat/test_measure_input_wide.R   |   7 +-
 tests/testthat/test_measure_output_long.R  |  11 +-
 tests/testthat/test_measure_output_wide.R  |   8 +-
 tests/testthat/test_savitzky_golay.R       | 111 ++++++++++-----------
 vignettes/baseline.Rmd                     |  28 +++---
 vignettes/recipes.Rmd                      |   2 +-
 17 files changed, 223 insertions(+), 210 deletions(-)

diff --git a/R/baseline.R b/R/baseline.R
index 57a12bf..a9f3191 100644
--- a/R/baseline.R
+++ b/R/baseline.R
@@ -70,17 +70,18 @@ print.step_baseline <-
 #'
 #' @examples
 #' meats_long %>% subtract_rf_baseline(yvar = transmittance)
-subtract_rf_baseline <- function(data, yvar, span = 2/3, maxit = c(5, 5)){
-
+subtract_rf_baseline <- function(data, yvar, span = 2 / 3, maxit = c(5, 5)) {
   # rlang::arg_match0(as.character(rlang::enquo(yvar)), values = names(data))
 
   data %>%
     dplyr::mutate(
       raw = {{ yvar }},
-      baseline = IDPmisc::rfbaseline(x = 1:length({{ yvar }}),
-                                     y = {{ yvar }},
-                                     span = span,
-                                     maxit = maxit)$fit,
+      baseline = IDPmisc::rfbaseline(
+        x = 1:length({{ yvar }}),
+        y = {{ yvar }},
+        span = span,
+        maxit = maxit
+      )$fit,
       {{ yvar }} := {{ yvar }} - baseline
     )
 }
diff --git a/R/checks.R b/R/checks.R
index e9e95d3..ed6fbc7 100644
--- a/R/checks.R
+++ b/R/checks.R
@@ -11,8 +11,10 @@ check_missing_measures <- function(.data, loc) {
 
 check_single_selector <- function(res, arg) {
   if (length(res) != 1) {
-    msg <- paste0("The selection for `", arg, "` should only select a single ",
-                  "column (", length(res), " columns were selected).")
+    msg <- paste0(
+      "The selection for `", arg, "` should only select a single ",
+      "column (", length(res), " columns were selected)."
+    )
     rlang::abort(msg)
   }
 }
@@ -39,14 +41,14 @@ pad_measure_dims <- function(x) {
   most_freq <- as.integer(names(num_unique)[1])
 
   # Pad each measure so they all have 'most_freq' rows
-  x$.measures <- purrr::map(x$.measures, ~{
+  x$.measures <- purrr::map(x$.measures, ~ {
     df <- .x
     if (nrow(df) < most_freq) {
       # Calculate how many rows to add
       rows_to_add <- most_freq - nrow(df)
       # Create a data frame with the required number of missing rows
       missing_rows <-
-        purrr::map_dfc(names(df), ~rep(NA_real_, rows_to_add)) %>%
+        purrr::map_dfc(names(df), ~ rep(NA_real_, rows_to_add)) %>%
         tibble::as_tibble() %>%
         setNames(names(df)) %>%
         suppressMessages() # suppress message about new column names
diff --git a/R/helpers.R b/R/helpers.R
index 9a8c979..69dabba 100644
--- a/R/helpers.R
+++ b/R/helpers.R
@@ -35,7 +35,7 @@ matrix_to_measure <- function(x, loc) {
   }
 
   x <- t(x)
-  x <-  tibble::as_tibble(x, .name_repair = "minimal")
+  x <- tibble::as_tibble(x, .name_repair = "minimal")
 
   res <- purrr::map(x, ~ tibble::new_tibble(list(location = loc, value = .x)))
   unname(res)
@@ -70,10 +70,12 @@ check_has_measure <- function(x, cl) {
 
   if (!any(names(x) == ".measures")) {
     msg <-
-      paste0("It appears that the measurements have not been converted ",
-             "for the inernal format. See `step_measure_input_long()` ",
-             "and `step_measure_input_wide()` and use these prior to ",
-             step_fn)
+      paste0(
+        "It appears that the measurements have not been converted ",
+        "for the inernal format. See `step_measure_input_long()` ",
+        "and `step_measure_input_wide()` and use these prior to ",
+        step_fn
+      )
     rlang::abort(msg)
   }
 }
diff --git a/R/input_long.R b/R/input_long.R
index d7cd715..4644cd6 100644
--- a/R/input_long.R
+++ b/R/input_long.R
@@ -154,12 +154,16 @@ print.step_measure_input_long <-
 #' @export
 tidy.step_measure_input_long <- function(x, ...) {
   if (is_trained(x)) {
-    res <- tibble(terms = x$columns[!is.na(x$columns)],
-                  value = na_dbl)
+    res <- tibble(
+      terms = x$columns[!is.na(x$columns)],
+      value = na_dbl
+    )
   } else {
     term_names <- sel2char(x$terms)
-    res <- tibble(terms = term_names,
-                  value = na_dbl)
+    res <- tibble(
+      terms = term_names,
+      value = na_dbl
+    )
   }
   res$id <- x$id
   res
@@ -173,5 +177,3 @@ rename_long_cols <- function(.data, val_chr, loc_chr) {
   }
   dplyr::rename(.data, dplyr::all_of(res))
 }
-
-
diff --git a/R/input_wide.R b/R/input_wide.R
index 1246029..46d7c7b 100644
--- a/R/input_wide.R
+++ b/R/input_wide.R
@@ -66,27 +66,27 @@
 #' @export
 
 step_measure_input_wide <-
-    function(recipe,
-             ...,
-             role = "measure",
-             trained = FALSE,
-             columns = NULL,
-             location_values = NULL,
-             skip = FALSE,
-             id = rand_id("measure_input_wide")) {
-      add_step(
-        recipe,
-        step_measure_input_wide_new(
-          terms = enquos(...),
-          trained = trained,
-          role = role,
-          columns = columns,
-          location_values = location_values,
-          skip = skip,
-          id = id
-        )
+  function(recipe,
+           ...,
+           role = "measure",
+           trained = FALSE,
+           columns = NULL,
+           location_values = NULL,
+           skip = FALSE,
+           id = rand_id("measure_input_wide")) {
+    add_step(
+      recipe,
+      step_measure_input_wide_new(
+        terms = enquos(...),
+        trained = trained,
+        role = role,
+        columns = columns,
+        location_values = location_values,
+        skip = skip,
+        id = id
       )
-    }
+    )
+  }
 
 step_measure_input_wide_new <-
   function(terms, role, trained, columns, location_values, skip, id) {
@@ -111,8 +111,10 @@ prep.step_measure_input_wide <- function(x, training, info = NULL, ...) {
     num_inputs <- length(col_names)
     num_loc <- length(x$location_values)
     if (num_inputs != num_loc) {
-      msg <- paste0(num_inputs, " columns were selected as inputs but ",
-                    "`location_values` has ", num_loc, " values.")
+      msg <- paste0(
+        num_inputs, " columns were selected as inputs but ",
+        "`location_values` has ", num_loc, " values."
+      )
       rlang::abort(msg)
     }
     # if
@@ -133,7 +135,6 @@ prep.step_measure_input_wide <- function(x, training, info = NULL, ...) {
 
 #' @export
 bake.step_measure_input_wide <- function(object, new_data, ...) {
-
   # TODO check to make sure that the nested tibble has the same number of rows
   # in case the nesting was bad
   wide_to_list(new_data, object$location_values, object$terms)
@@ -151,12 +152,16 @@ print.step_measure_input_wide <-
 #' @export
 tidy.step_measure_input_wide <- function(x, ...) {
   if (is_trained(x)) {
-    res <- tibble(terms = x$columns,
-                  value = na_dbl)
+    res <- tibble(
+      terms = x$columns,
+      value = na_dbl
+    )
   } else {
     term_names <- sel2char(x$terms)
-    res <- tibble(terms = term_names,
-                  value = na_dbl)
+    res <- tibble(
+      terms = term_names,
+      value = na_dbl
+    )
   }
   res$id <- x$id
   res
diff --git a/R/output_long.R b/R/output_long.R
index a35da42..2f7b03a 100644
--- a/R/output_long.R
+++ b/R/output_long.R
@@ -19,11 +19,11 @@
 #' data(glucose_bioreactors)
 #' bioreactors_small$batch_sample <- NULL
 #'
-#' small_tr <- bioreactors_small[  1:200,]
-#' small_te <- bioreactors_small[201:210,]
+#' small_tr <- bioreactors_small[1:200, ]
+#' small_te <- bioreactors_small[201:210, ]
 #'
 #' small_rec <-
-#'   recipe(glucose ~ . , data = small_tr) %>%
+#'   recipe(glucose ~ ., data = small_tr) %>%
 #'   update_role(batch_id, day, new_role = "id columns") %>%
 #'   step_measure_input_wide(`400`:`3050`) %>%
 #'   prep()
@@ -103,8 +103,10 @@ bake.step_measure_output_long <- function(object, new_data, ...) {
 print.step_measure_output_long <-
   function(x, width = max(20, options()$width - 30), ...) {
     title <- "Restructure analytical measurements to long format"
-    print_step(rlang::quos("<internal data>"), rlang::quos("<internal data>"),
-               x$trained, title, width)
+    print_step(
+      rlang::quos("<internal data>"), rlang::quos("<internal data>"),
+      x$trained, title, width
+    )
     invisible(x)
   }
 
@@ -112,11 +114,15 @@ print.step_measure_output_long <-
 #' @export
 tidy.step_measure_output_long <- function(x, ...) {
   if (is_trained(x)) {
-    res <- tibble(terms = na_chr,
-                  value = na_dbl)
+    res <- tibble(
+      terms = na_chr,
+      value = na_dbl
+    )
   } else {
-    res <- tibble(terms = na_chr,
-                  value = na_dbl)
+    res <- tibble(
+      terms = na_chr,
+      value = na_dbl
+    )
   }
   res$id <- x$id
   res
@@ -127,5 +133,3 @@ value_to_tibble <- function(x, prefix = "measure_") {
   colnames(x) <- recipes::names0(ncol(x), prefix = prefix)
   dplyr::as_tibble(x)
 }
-
-
diff --git a/R/output_wide.R b/R/output_wide.R
index c5f022e..b30ac98 100644
--- a/R/output_wide.R
+++ b/R/output_wide.R
@@ -18,11 +18,11 @@
 #' data(glucose_bioreactors)
 #' bioreactors_small$batch_sample <- NULL
 #'
-#' small_tr <- bioreactors_small[  1:200,]
-#' small_te <- bioreactors_small[201:210,]
+#' small_tr <- bioreactors_small[1:200, ]
+#' small_te <- bioreactors_small[201:210, ]
 #'
 #' small_rec <-
-#'   recipe(glucose ~ . , data = small_tr) %>%
+#'   recipe(glucose ~ ., data = small_tr) %>%
 #'   update_role(batch_id, day, new_role = "id columns") %>%
 #'   step_measure_input_wide(`400`:`3050`) %>%
 #'   prep()
@@ -87,7 +87,6 @@ prep.step_measure_output_wide <- function(x, training, info = NULL, ...) {
 
 #' @export
 bake.step_measure_output_wide <- function(object, new_data, ...) {
-
   non_meas <- names(new_data)
   non_meas <- non_meas[non_meas != ".measures"]
 
@@ -117,13 +116,16 @@ print.step_measure_output_wide <-
 #' @export
 tidy.step_measure_output_wide <- function(x, ...) {
   if (is_trained(x)) {
-    res <- tibble(terms = na_chr,
-                  value = na_dbl)
+    res <- tibble(
+      terms = na_chr,
+      value = na_dbl
+    )
   } else {
-    res <- tibble(terms = na_chr,
-                  value = na_dbl)
+    res <- tibble(
+      terms = na_chr,
+      value = na_dbl
+    )
   }
   res$id <- x$id
   res
 }
-
diff --git a/R/savitzky_golay.R b/R/savitzky_golay.R
index 65e475b..153bbb4 100644
--- a/R/savitzky_golay.R
+++ b/R/savitzky_golay.R
@@ -61,29 +61,28 @@
 #'     ) %>%
 #'     prep()
 #' }
-
 step_measure_savitzky_golay <-
-    function(recipe,
-             role = NA,
-             trained = FALSE,
-             degree = 3,
-             window_size = 11,
-             differentiation_order = 0,
-             skip = FALSE,
-             id = rand_id("measure_savitzky_golay")) {
-      recipes::add_step(
-        recipe,
-        step_measure_savitzky_golay_new(
-          trained = trained,
-          role = role,
-          degree = degree,
-          window_size = window_size,
-          differentiation_order = differentiation_order,
-          skip = FALSE,
-          id = id
-        )
+  function(recipe,
+           role = NA,
+           trained = FALSE,
+           degree = 3,
+           window_size = 11,
+           differentiation_order = 0,
+           skip = FALSE,
+           id = rand_id("measure_savitzky_golay")) {
+    recipes::add_step(
+      recipe,
+      step_measure_savitzky_golay_new(
+        trained = trained,
+        role = role,
+        degree = degree,
+        window_size = window_size,
+        differentiation_order = differentiation_order,
+        skip = FALSE,
+        id = id
       )
-    }
+    )
+  }
 
 step_measure_savitzky_golay_new <-
   function(role, trained, degree, window_size, differentiation_order,
@@ -107,14 +106,14 @@ prep.step_measure_savitzky_golay <- function(x, training, info = NULL, ...) {
     cli::cli_abort("{.arg degree} to {.fn  step_measure_savitzky_golay} should
                     be a single integer greater than zero.")
   }
-  if (!is.numeric(x$differentiation_order) | length(x$differentiation_order) != 1
-      | x$differentiation_order < 0) {
+  if (!is.numeric(x$differentiation_order) | length(x$differentiation_order) != 1 |
+    x$differentiation_order < 0) {
     cli::cli_abort("The {.arg differentiation_order} argument to
                     {.fn  step_measure_savitzky_golay} should be a single
                     integer greater than -1.")
   }
-  if (!is.numeric(x$window_size) | length(x$window_size) != 1
-      | x$window_size < 1 | x$window_size %% 2 != 1) {
+  if (!is.numeric(x$window_size) | length(x$window_size) != 1 |
+    x$window_size < 1 | x$window_size %% 2 != 1) {
     cli::cli_abort("The {.arg window_size} argument to
                     {.fn  step_measure_savitzky_golay} should be a single odd
                     integer greater than 0.")
@@ -130,10 +129,10 @@ prep.step_measure_savitzky_golay <- function(x, training, info = NULL, ...) {
   }
   # filter length w must be greater than polynomial order p
   if (x$window_size <= x$degree) {
-     x$window_size <- x$degree + 1
-     if (x$window_size %% 2 == 0) {
-       x$window_size <- x$window_size + 1
-     }
+    x$window_size <- x$degree + 1
+    if (x$window_size %% 2 == 0) {
+      x$window_size <- x$window_size + 1
+    }
     cli::cli_warn("The {.arg window_size} argument to
                    {.fn step_measure_savitzky_golay} should be greater than or
                    equal to {.arg degree}. The polynomial degree was increased
@@ -153,7 +152,6 @@ prep.step_measure_savitzky_golay <- function(x, training, info = NULL, ...) {
 
 #' @export
 bake.step_measure_savitzky_golay <- function(object, new_data, ...) {
-
   res <-
     .comp_savitzky_golay(
       new_data$.measures,
@@ -170,8 +168,10 @@ bake.step_measure_savitzky_golay <- function(object, new_data, ...) {
 print.step_measure_savitzky_golay <-
   function(x, width = max(20, options()$width - 30), ...) {
     title <- "Savitzky-Golay preprocessing "
-    recipes::print_step("<internal measurements>", "<internal measurements>",
-                        x$trained, title, width)
+    recipes::print_step(
+      "<internal measurements>", "<internal measurements>",
+      x$trained, title, width
+    )
     invisible(x)
   }
 
@@ -181,12 +181,16 @@ print.step_measure_savitzky_golay <-
 #' @export
 tidy.step_measure_savitzky_golay <- function(x, ...) {
   if (is_trained(x)) {
-    res <- tibble::tibble(terms = ".measure",
-                          value = na_dbl)
+    res <- tibble::tibble(
+      terms = ".measure",
+      value = na_dbl
+    )
   } else {
     term_names <- recipes::sel2char(x$terms)
-    res <- tibble::tibble(terms = term_names,
-                          value = na_dbl)
+    res <- tibble::tibble(
+      terms = term_names,
+      value = na_dbl
+    )
   }
   res$id <- x$id
   res
@@ -235,4 +239,3 @@ required_pkgs.step_isomap <- function(x, ...) {
 
   matrix_to_measure(res, loc)
 }
-
diff --git a/tests/testthat/helpers-data.R b/tests/testthat/helpers-data.R
index 69c1c6f..f5767ce 100644
--- a/tests/testthat/helpers-data.R
+++ b/tests/testthat/helpers-data.R
@@ -5,8 +5,10 @@ data_meat_long <- function() {
   library(tidyr)
   library(dplyr)
 
-  inds <- tibble(temp = grep("^x_", names(meats), value = TRUE),
-                 ind = seq(1, 17, length.out = 100))
+  inds <- tibble(
+    temp = grep("^x_", names(meats), value = TRUE),
+    ind = seq(1, 17, length.out = 100)
+  )
 
   meats_2 <-
     meats %>%
@@ -19,13 +21,15 @@ data_meat_long <- function() {
     full_join(inds, by = "temp") %>%
     select(-temp)
 
-  inds <- tibble(temp = grep("^x_", names(meats), value = TRUE),
-                 ind = seq(1, 17, length.out = 100))
+  inds <- tibble(
+    temp = grep("^x_", names(meats), value = TRUE),
+    ind = seq(1, 17, length.out = 100)
+  )
 
   list(
     train = meats_2 %>% filter(.sample_num <= 200),
-    test  = meats_2 %>% filter(.sample_num >  200)
-    )
+    test  = meats_2 %>% filter(.sample_num > 200)
+  )
 }
 
 data_meat_wide <- function() {
@@ -42,10 +46,7 @@ data_meat_wide <- function() {
 
   list(
     train = meats_2 %>% filter(.sample_num <= 200),
-    test  = meats_2 %>% filter(.sample_num >  200),
+    test = meats_2 %>% filter(.sample_num > 200),
     ind = seq(1, 17, length.out = 100)
   )
 }
-
-
-
diff --git a/tests/testthat/test-data-transformations.R b/tests/testthat/test-data-transformations.R
index 6ff2a6c..fe5df1c 100644
--- a/tests/testthat/test-data-transformations.R
+++ b/tests/testthat/test-data-transformations.R
@@ -1,5 +1,4 @@
 test_that("transform measure to matrix", {
-
   rec <-
     recipe(water + fat + protein ~ ., data = meats_long) %>%
     update_role(id, new_role = "id") %>%
@@ -18,11 +17,9 @@ test_that("transform measure to matrix", {
       meats_long[meats_long$id == ids[i], "transmittance"][[1]]
     )
   }
-
 })
 
 test_that("transform matrix to measure", {
-
   rec <-
     recipe(water + fat + protein ~ ., data = meats_long) %>%
     update_role(id, new_role = "id") %>%
@@ -41,11 +38,9 @@ test_that("transform matrix to measure", {
       rec$template$.measures[[i]]
     )
   }
-
 })
 
 test_that("transform tidy format", {
-
   rec <-
     recipe(water + fat + protein ~ ., data = meats_long) %>%
     update_role(id, new_role = "id") %>%
@@ -57,5 +52,4 @@ test_that("transform tidy format", {
   names(exp_df) <- c("location", "value", "sample_num")
 
   expect_equal(spect_df, exp_df)
-
 })
diff --git a/tests/testthat/test_measure_input_long.R b/tests/testthat/test_measure_input_long.R
index 1aa20c1..988559a 100644
--- a/tests/testthat/test_measure_input_long.R
+++ b/tests/testthat/test_measure_input_long.R
@@ -7,7 +7,7 @@ test_that("ingest long format data", {
   na_test$absorp[2] <- NA_real_
 
   miss_train <- meats_data$train %>% dplyr::slice(-5)
-  miss_test  <- meats_data$test  %>% dplyr::slice(-5)
+  miss_test <- meats_data$test %>% dplyr::slice(-5)
 
   # ----------------------------------------------------------------------------
 
@@ -32,18 +32,18 @@ test_that("ingest long format data", {
       protein = numeric(0),
       .measures = list()
     )
-  expect_equal(bake_1[0,], dat_ptype)
+  expect_equal(bake_1[0, ], dat_ptype)
   measure_ptype <-
     tibble::tibble(
       value = numeric(0),
       location = numeric(0)
     )
-  expect_equal(bake_1$.measures[[1]][0,], measure_ptype)
+  expect_equal(bake_1$.measures[[1]][0, ], measure_ptype)
   expect_equal(nrow(bake_1), 200L)
   expect_equal(dim(bake_1$.measures[[1]]), c(100L, 2L))
 
   bake_1_te <- bake(prep_1, new_data = meats_data$test)
-  expect_equal(bake_1_te$.measures[[1]][0,], measure_ptype)
+  expect_equal(bake_1_te$.measures[[1]][0, ], measure_ptype)
   expect_equal(nrow(bake_1_te), 15L)
   expect_equal(dim(bake_1_te$.measures[[1]]), c(100L, 2L))
 
diff --git a/tests/testthat/test_measure_input_wide.R b/tests/testthat/test_measure_input_wide.R
index 154cb94..5887323 100644
--- a/tests/testthat/test_measure_input_wide.R
+++ b/tests/testthat/test_measure_input_wide.R
@@ -29,18 +29,18 @@ test_that("ingest wide format data", {
       protein = numeric(0),
       .measures = list()
     )
-  expect_equal(bake_1[0,], dat_ptype)
+  expect_equal(bake_1[0, ], dat_ptype)
   measure_ptype <-
     tibble::tibble(
       value = numeric(0),
       location = numeric(0)
     )
-  expect_equal(bake_1$.measures[[1]][0,], measure_ptype)
+  expect_equal(bake_1$.measures[[1]][0, ], measure_ptype)
   expect_equal(nrow(bake_1), 200L)
   expect_equal(dim(bake_1$.measures[[1]]), c(100L, 2L))
 
   bake_1_te <- bake(prep_1, new_data = meats_data$test)
-  expect_equal(bake_1_te$.measures[[1]][0,], measure_ptype)
+  expect_equal(bake_1_te$.measures[[1]][0, ], measure_ptype)
   expect_equal(nrow(bake_1_te), 15L)
   expect_equal(dim(bake_1_te$.measures[[1]]), c(100L, 2L))
 
@@ -58,5 +58,4 @@ test_that("ingest wide format data", {
       prep(),
     error = TRUE
   )
-
 })
diff --git a/tests/testthat/test_measure_output_long.R b/tests/testthat/test_measure_output_long.R
index c464712..f6cfbb4 100644
--- a/tests/testthat/test_measure_output_long.R
+++ b/tests/testthat/test_measure_output_long.R
@@ -1,7 +1,7 @@
 test_that("output long format data", {
   meats_data <- data_meat_long()
   meats_train <- meats_data$train %>% filter(ind < 1.2)
-  meats_test  <- meats_data$test  %>% filter(ind < 1.2)
+  meats_test <- meats_data$test %>% filter(ind < 1.2)
 
   na_train <- meats_train
   na_train$absorp[1] <- NA_real_
@@ -9,7 +9,7 @@ test_that("output long format data", {
   na_test$absorp[1] <- NA_real_
 
   miss_train <- meats_train %>% dplyr::slice(-2)
-  miss_test  <- meats_test  %>% dplyr::slice(-2)
+  miss_test <- meats_test %>% dplyr::slice(-2)
 
   # ----------------------------------------------------------------------------
 
@@ -36,11 +36,11 @@ test_that("output long format data", {
       .measure = numeric(0),
       .location = numeric(0)
     )
-  expect_equal(bake_1[0,], dat_ptype)
+  expect_equal(bake_1[0, ], dat_ptype)
   expect_equal(nrow(bake_1), 400L)
 
   bake_1_te <- bake(prep_1, new_data = meats_test)
-  expect_equal(bake_1_te[0,], dat_ptype)
+  expect_equal(bake_1_te[0, ], dat_ptype)
   expect_equal(nrow(bake_1_te), 30L)
 
   ### missing rows
@@ -70,7 +70,7 @@ test_that("output long format data", {
       rstudio = numeric(0),
       posit = numeric(0)
     )
-  expect_equal(bake_2[0,], dat_ptype)
+  expect_equal(bake_2[0, ], dat_ptype)
   expect_equal(nrow(bake_2), 400L)
 
   ## missing values
@@ -92,5 +92,4 @@ test_that("output long format data", {
       prep(),
     error = TRUE
   )
-
 })
diff --git a/tests/testthat/test_measure_output_wide.R b/tests/testthat/test_measure_output_wide.R
index 2754cb2..fc84ef9 100644
--- a/tests/testthat/test_measure_output_wide.R
+++ b/tests/testthat/test_measure_output_wide.R
@@ -1,7 +1,7 @@
 test_that("output wide format data", {
   meats_data <- data_meat_long()
   meats_train <- meats_data$train %>% filter(ind < 1.2)
-  meats_test  <- meats_data$test  %>% filter(ind < 1.2)
+  meats_test <- meats_data$test %>% filter(ind < 1.2)
 
   na_train <- meats_train
   na_train$absorp[1] <- NA_real_
@@ -9,7 +9,7 @@ test_that("output wide format data", {
   na_test$absorp[1] <- NA_real_
 
   miss_train <- meats_train %>% dplyr::slice(-2)
-  miss_test  <- meats_test  %>% dplyr::slice(-2)
+  miss_test <- meats_test %>% dplyr::slice(-2)
 
   # ----------------------------------------------------------------------------
 
@@ -36,11 +36,11 @@ test_that("output wide format data", {
       measure_1.000000 = numeric(0),
       measure_1.161616 = numeric(0)
     )
-  expect_equal(bake_1[0,], dat_ptype)
+  expect_equal(bake_1[0, ], dat_ptype)
   expect_equal(nrow(bake_1), 200L)
 
   bake_1_te <- bake(prep_1, new_data = meats_test)
-  expect_equal(bake_1_te[0,], dat_ptype)
+  expect_equal(bake_1_te[0, ], dat_ptype)
   expect_equal(nrow(bake_1_te), 15L)
 
   ### missing rows
diff --git a/tests/testthat/test_savitzky_golay.R b/tests/testthat/test_savitzky_golay.R
index eaf6a11..837585e 100644
--- a/tests/testthat/test_savitzky_golay.R
+++ b/tests/testthat/test_savitzky_golay.R
@@ -26,12 +26,12 @@ test_that("savitzky-golay computations", {
       measure:::measure_to_matrix()
     prosp_res <-
       prospectr::savitzkyGolay(spect_start,
-                               m = grid$diffs[i],
-                               p = grid$deg[i],
-                               w = grid$wn[i])
+        m = grid$diffs[i],
+        p = grid$deg[i],
+        w = grid$wn[i]
+      )
     expect_equal(meas_res, prosp_res)
   }
-
 })
 
 test_that("savitzky-golay inputs", {
@@ -50,60 +50,60 @@ test_that("savitzky-golay inputs", {
   bad_inputs <-
     tibble::tribble(
       ~diffs, ~deg, ~wn,
-      2L,   1L,   5,
-      3L,   1L,   5,
-      3L,   2L,   5,
-      0L,   5L,   5,
-      1L,   5L,   5,
-      2L,   5L,   5,
-      3L,   5L,   5,
-      0L,   6L,   5,
-      1L,   6L,   5,
-      2L,   6L,   5,
-      3L,   6L,   5,
-      0L,   1L,  10,
-      1L,   1L,  10,
-      2L,   1L,  10,
-      3L,   1L,  10,
-      0L,   2L,  10,
-      1L,   2L,  10,
-      2L,   2L,  10,
-      3L,   2L,  10,
-      0L,   3L,  10,
-      1L,   3L,  10,
-      2L,   3L,  10,
-      3L,   3L,  10,
-      0L,   4L,  10,
-      1L,   4L,  10,
-      2L,   4L,  10,
-      3L,   4L,  10,
-      0L,   5L,  10,
-      1L,   5L,  10,
-      2L,   5L,  10,
-      3L,   5L,  10,
-      0L,   6L,  10,
-      1L,   6L,  10,
-      2L,   6L,  10,
-      3L,   6L,  10,
-      2L,   1L,  15,
-      3L,   1L,  15,
-      3L,   2L,  15
+      2L, 1L, 5,
+      3L, 1L, 5,
+      3L, 2L, 5,
+      0L, 5L, 5,
+      1L, 5L, 5,
+      2L, 5L, 5,
+      3L, 5L, 5,
+      0L, 6L, 5,
+      1L, 6L, 5,
+      2L, 6L, 5,
+      3L, 6L, 5,
+      0L, 1L, 10,
+      1L, 1L, 10,
+      2L, 1L, 10,
+      3L, 1L, 10,
+      0L, 2L, 10,
+      1L, 2L, 10,
+      2L, 2L, 10,
+      3L, 2L, 10,
+      0L, 3L, 10,
+      1L, 3L, 10,
+      2L, 3L, 10,
+      3L, 3L, 10,
+      0L, 4L, 10,
+      1L, 4L, 10,
+      2L, 4L, 10,
+      3L, 4L, 10,
+      0L, 5L, 10,
+      1L, 5L, 10,
+      2L, 5L, 10,
+      3L, 5L, 10,
+      0L, 6L, 10,
+      1L, 6L, 10,
+      2L, 6L, 10,
+      3L, 6L, 10,
+      2L, 1L, 15,
+      3L, 1L, 15,
+      3L, 2L, 15
     )
 
   for (i in 1:nrow(bad_inputs)) {
-
     if (bad_inputs$wn[i] == 10) {
-      expect_snapshot({
-        rec %>%
-          step_measure_savitzky_golay(
-            differentiation_order = bad_inputs$diffs[i],
-            window_size = bad_inputs$wn[i],
-            degree = bad_inputs$deg[i]
-          ) %>%
-          prep()
-      },
-      error = TRUE)
-
+      expect_snapshot(
+        {
+          rec %>%
+            step_measure_savitzky_golay(
+              differentiation_order = bad_inputs$diffs[i],
+              window_size = bad_inputs$wn[i],
+              degree = bad_inputs$deg[i]
+            ) %>%
+            prep()
+        },
+        error = TRUE
+      )
     } else {
       expect_snapshot_warning({
         rec %>%
@@ -115,8 +115,5 @@ test_that("savitzky-golay inputs", {
           prep()
       })
     }
-
   }
-
 })
-
diff --git a/vignettes/baseline.Rmd b/vignettes/baseline.Rmd
index 5f596b0..e061c59 100644
--- a/vignettes/baseline.Rmd
+++ b/vignettes/baseline.Rmd
@@ -29,30 +29,32 @@ theme_set(theme_light())
 Before we can perform baseline correction, we need to reshape the data. It is in a wide format where the columns represent the wavelength and the value is transmittance. The `step_baseline()` function operates on long format data. We can reshape this data with `{tidyr}`.
 
 ```{r}
-meats2 <- 
+meats2 <-
   meats %>%
-  rowid_to_column(var = "id") %>% 
-  pivot_longer(cols = starts_with("x_"),
-               names_to = "channel",
-               values_to = "transmittance") %>% 
+  rowid_to_column(var = "id") %>%
+  pivot_longer(
+    cols = starts_with("x_"),
+    names_to = "channel",
+    values_to = "transmittance"
+  ) %>%
   mutate(channel = str_extract(channel, "[:digit:]+") %>% as.integer())
 ```
 
 ```{r}
 meats2 %>%
-  ggplot(aes(x = channel, y = transmittance, group = id)) + 
-  geom_line(alpha = 0.5) + theme_light()
+  ggplot(aes(x = channel, y = transmittance, group = id)) +
+  geom_line(alpha = 0.5) +
+  theme_light()
 ```
 
 
 ```{r}
-meats2 %>% 
-  group_by(id) %>% 
-  subtract_rf_baseline(yvar = transmittance, span = 0.8) %>% 
-  ggplot(aes(x = channel, color = water, group = id)) + 
+meats2 %>%
+  group_by(id) %>%
+  subtract_rf_baseline(yvar = transmittance, span = 0.8) %>%
+  ggplot(aes(x = channel, color = water, group = id)) +
   geom_line(aes(y = transmittance), alpha = 0.5) +
-  scale_color_viridis_c() + 
+  scale_color_viridis_c() +
   ggtitle("")
-
 ```
 
diff --git a/vignettes/recipes.Rmd b/vignettes/recipes.Rmd
index 830740d..ae8ae5c 100644
--- a/vignettes/recipes.Rmd
+++ b/vignettes/recipes.Rmd
@@ -58,7 +58,7 @@ The recipe does not yet contain any steps.
 ```{r}
 rec_obj$steps
 
-rec_obj_add_step <- rec_obj %>% 
+rec_obj_add_step <- rec_obj %>%
   step_impute_knn(all_predictors())
 
 rec_obj_add_step$steps

From 7e410b41c061f5ca6ea1529dbf90f2427df7f4f8 Mon Sep 17 00:00:00 2001
From: James Wade <jhwade@dow.com>
Date: Fri, 2 Feb 2024 14:39:43 -0500
Subject: [PATCH 11/11] [docs] style man pages

---
 man/step_measure_output_long.Rd | 6 +++---
 man/step_measure_output_wide.Rd | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/man/step_measure_output_long.Rd b/man/step_measure_output_long.Rd
index 94dfe1b..95367c8 100644
--- a/man/step_measure_output_long.Rd
+++ b/man/step_measure_output_long.Rd
@@ -54,11 +54,11 @@ library(dplyr)
 data(glucose_bioreactors)
 bioreactors_small$batch_sample <- NULL
 
-small_tr <- bioreactors_small[  1:200,]
-small_te <- bioreactors_small[201:210,]
+small_tr <- bioreactors_small[1:200, ]
+small_te <- bioreactors_small[201:210, ]
 
 small_rec <-
-  recipe(glucose ~ . , data = small_tr) \%>\%
+  recipe(glucose ~ ., data = small_tr) \%>\%
   update_role(batch_id, day, new_role = "id columns") \%>\%
   step_measure_input_wide(`400`:`3050`) \%>\%
   prep()
diff --git a/man/step_measure_output_wide.Rd b/man/step_measure_output_wide.Rd
index abeca9d..2836518 100644
--- a/man/step_measure_output_wide.Rd
+++ b/man/step_measure_output_wide.Rd
@@ -52,11 +52,11 @@ library(dplyr)
 data(glucose_bioreactors)
 bioreactors_small$batch_sample <- NULL
 
-small_tr <- bioreactors_small[  1:200,]
-small_te <- bioreactors_small[201:210,]
+small_tr <- bioreactors_small[1:200, ]
+small_te <- bioreactors_small[201:210, ]
 
 small_rec <-
-  recipe(glucose ~ . , data = small_tr) \%>\%
+  recipe(glucose ~ ., data = small_tr) \%>\%
   update_role(batch_id, day, new_role = "id columns") \%>\%
   step_measure_input_wide(`400`:`3050`) \%>\%
   prep()