From 610e5d4459610217fa461576f2a87338592525e7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=98topepo=E2=80=99?= <‘mxkuhn@gmail.com’>
Date: Wed, 3 Jan 2024 12:58:49 -0500
Subject: [PATCH 01/13] initial work on Savitzky-Golay filter

---
 DESCRIPTION                          |   2 +-
 NAMESPACE                            |   7 ++
 R/baseline.R                         |   2 +
 R/helpers.R                          |  36 ++++++
 R/savitzky_golay.R                   | 161 +++++++++++++++++++++++++++
 man/step_measure_savitzky_golay.Rd   |  62 +++++++++++
 tests/testthat/test_savitzky_golay.R |   0
 7 files changed, 269 insertions(+), 1 deletion(-)
 create mode 100644 R/savitzky_golay.R
 create mode 100644 man/step_measure_savitzky_golay.Rd
 create mode 100644 tests/testthat/test_savitzky_golay.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 007401c..14e8677 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -31,7 +31,7 @@ Suggests:
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.2.3.9000
 VignetteBuilder: knitr
 Depends: 
     R (>= 3.5.0),
diff --git a/NAMESPACE b/NAMESPACE
index df7da00..732fdf2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,16 +1,23 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(bake,step_baseline)
 S3method(bake,step_measure_input_long)
 S3method(bake,step_measure_input_wide)
+S3method(bake,step_measure_savitzky_golay)
+S3method(prep,step_baseline)
 S3method(prep,step_measure_input_long)
 S3method(prep,step_measure_input_wide)
+S3method(prep,step_measure_savitzky_golay)
 S3method(print,step_baseline)
 S3method(print,step_measure_input_long)
 S3method(print,step_measure_input_wide)
+S3method(print,step_measure_savitzky_golay)
 S3method(tidy,step_measure_input_long)
 S3method(tidy,step_measure_input_wide)
+S3method(tidy,step_measure_savitzky_golay)
 export(step_measure_input_long)
 export(step_measure_input_wide)
+export(step_measure_savitzky_golay)
 export(subtract_rf_baseline)
 import(recipes)
 import(rlang)
diff --git a/R/baseline.R b/R/baseline.R
index 235bdfd..57a12bf 100644
--- a/R/baseline.R
+++ b/R/baseline.R
@@ -41,6 +41,7 @@ step_baseline_new <-
     )
   }
 
+#' @export
 prep.step_baseline <- function(x, training, info = NULL, ...) {
   col_names <- recipes::recipes_eval_select(x$terms, training, info)
   recipes::check_type(x, quant = TRUE)
@@ -84,6 +85,7 @@ subtract_rf_baseline <- function(data, yvar, span = 2/3, maxit = c(5, 5)){
     )
 }
 
+#' @export
 bake.step_baseline <- function(object, new_data, ...) {
   cli::cli_alert_danger("Not yet implemented.")
 }
diff --git a/R/helpers.R b/R/helpers.R
index 78e9924..4945063 100644
--- a/R/helpers.R
+++ b/R/helpers.R
@@ -12,3 +12,39 @@ add_location <- function(.data, loc) {
     .measures = purrr::map(.measures, add_location_col, loc = loc)
   )
 }
+
+# ------------------------------------------------------------------------------
+# Move between lists of tibbles and matrices (and back)
+
+# Assumes identical locations
+measure_to_matrix <- function(x) {
+  n <- length(x)
+  loc <- x[[1]]$location
+  res <- do.call("rbind", purrr::map(x, ~ .x[["value"]]))
+  res
+}
+
+matrix_to_measure <- function(x, loc) {
+  # x is {num_samples} x {num_features}
+  # We need to convert this to a list of length {num_samples}.
+  # Each list element is a tibble that is {num_features} x 2
+  if (!is.matrix(x)) {
+    cli::cli_abort("Input should be a matrix.")
+  }
+  if (length(loc) != ncol(x)) {
+    cli::cli_abort("# locations should be the same at the number of columns in the source matrix.")
+  }
+
+  x <- t(x)
+  x <-  tibble::as_tibble(x, .name_repair = "minimal")
+
+  res <- purrr::map(x, ~ tibble::new_tibble(list(value = .x, location = loc)))
+  unname(res)
+}
+
+measure_to_tibble <- function(x) {
+  x <-
+    tibble::tibble(x = sg, sample_num = seq_along(x)) %>%
+    tidyr::unnest(cols = x)
+  x
+}
diff --git a/R/savitzky_golay.R b/R/savitzky_golay.R
new file mode 100644
index 0000000..c43794c
--- /dev/null
+++ b/R/savitzky_golay.R
@@ -0,0 +1,161 @@
+#' Savitzky-Golay Pre-Processing
+#'
+#' `step_measure_savitzky_golay` creates a *specification* of a recipe
+#'  step that <what it does>
+#'
+#' @param recipe A recipe object. The step will be added to the
+#'  sequence of operations for this recipe.
+#' @param ... One or more selector functions to choose which
+#'  variables are affected by the step. See [selections()]
+#'  for more details. For the `tidy` method, these are not
+#'  currently used.
+#' @param role Not used by this step since no new variables are
+#'  created. <change if role is used>
+#' @param trained A logical to indicate if the quantities for
+#'  preprocessing have been estimated.
+#' @param degree The polynomial degree to use for smoothing.
+#' @param window_size The window size to use for smoothing.
+#' @param differentiation_order An integer for the degree of filtering (zero
+#' indicates no differentiation).
+#' @param skip A logical. Should the step be skipped when the
+#'  recipe is baked by [bake()]? While all operations are baked
+#'  when [prep()] is run, some operations may not be able to be
+#'  conducted on new data (e.g. processing the outcome variable(s)).
+#'  Care should be taken when using `skip = TRUE` as it may affect
+#'  the computations for subsequent operations
+#' @param id A character string that is unique to this step to identify it.
+#' @return An updated version of `recipe` with the new step added to the
+#' sequence of any existing operations.
+#'
+#' @export
+#' @details
+#'
+#' # Tidying
+#'
+#' When you [`tidy()`][tidy.recipe()] this step, a tibble with columns
+#' <describe tidying> is returned.
+#'
+# @examples
+
+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(
+          terms = enquos(...),
+          trained = trained,
+          role = role,
+          degree = degree,
+          window_size = window_size,
+          differentiation_order = differentiation_order,
+          skip = FALSE,
+          id = id
+        )
+      )
+    }
+
+step_measure_savitzky_golay_new <-
+  function(terms, role, trained, degree, window_size, differentiation_order,
+           na_rm, skip, id) {
+    recipes::step(
+      subclass = "measure_savitzky_golay",
+      terms = terms,
+      role = role,
+      trained = trained,
+      degree = degree,
+      window_size = window_size,
+      differentiation_order = differentiation_order,
+      skip = skip,
+      id = id
+    )
+  }
+
+#' @export
+prep.step_measure_savitzky_golay <- function(x, training, info = NULL, ...) {
+  col_names <- recipes::recipes_eval_select(x$terms, training, info)
+  recipes::check_type(training[, col_names])
+
+  step_measure_savitzky_golay_new(
+    terms = x$terms,
+    role = x$role,
+    trained = TRUE,
+    degree = x$degree,
+    window_size = x$window_size,
+    differentiation_order = x$differentiation_order,
+    skip = x$skip,
+    id = x$id
+  )
+}
+
+#' @export
+bake.step_measure_savitzky_golay <- function(object, new_data, ...) {
+
+  res <-
+    .comp_savitzky_golay(
+      new_data$.measures,
+      diffs = object$differentiation_order,
+      degree = object$degree,
+      window = object$window_size
+    )
+  new_data$.measures <- res
+  tibble::as_tibble(new_data)
+}
+
+#' @export
+print.step_measure_savitzky_golay <-
+  function(x, width = max(20, options()$width - 30), ...) {
+    title <- "Savitzky-Golay preprocessing "
+    recipes::print_step(names(x$means), x$terms, x$trained, title, width)
+    invisible(x)
+  }
+
+#' @rdname measure-tidy.recipe
+#' @export
+tidy.step_measure_savitzky_golay <- function(x, ...) {
+  if (is_trained(x)) {
+    res <- tibble::tibble(terms = ".measure",
+                          value = na_dbl)
+  } else {
+    term_names <- recipes::sel2char(x$terms)
+    res <- tibble::tibble(terms = term_names,
+                          value = na_dbl)
+  }
+  res$id <- x$id
+  res
+}
+
+# ------------------------------------------------------------------------------
+
+.comp_savitzky_golay <- function(dat, diffs = 1, degree = 2, window = 3, ...) {
+  rlang::check_installed("prospectr")
+  loc <- dat[[1]]$location
+  dat <- measure_to_matrix(dat)
+
+  cl <-
+    rlang::call2(
+      "savitzkyGolay",
+      .ns = "prospectr",
+      X = expr(dat),
+      m = diffs,
+      p = degree,
+      w = window,
+      ...
+    )
+  res <- rlang::eval_tidy(cl)
+
+  if (ncol(res) != ncol(dat)) {
+    # Prob can do better
+    loc <- 1:ncol(res)
+  }
+
+  matrix_to_measure(res, loc)
+}
+
diff --git a/man/step_measure_savitzky_golay.Rd b/man/step_measure_savitzky_golay.Rd
new file mode 100644
index 0000000..045e988
--- /dev/null
+++ b/man/step_measure_savitzky_golay.Rd
@@ -0,0 +1,62 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/savitzky_golay.R
+\name{step_measure_savitzky_golay}
+\alias{step_measure_savitzky_golay}
+\title{Savitzky-Golay Pre-Processing}
+\usage{
+step_measure_savitzky_golay(
+  recipe,
+  ...,
+  role = NA,
+  trained = FALSE,
+  degree = 3,
+  window_size = 11,
+  differentiation_order = 0,
+  skip = FALSE,
+  id = rand_id("measure_savitzky_golay")
+)
+}
+\arguments{
+\item{recipe}{A recipe object. The step will be added to the
+sequence of operations for this recipe.}
+
+\item{...}{One or more selector functions to choose which
+variables are affected by the step. See \code{\link[=selections]{selections()}}
+for more details. For the \code{tidy} method, these are not
+currently used.}
+
+\item{role}{Not used by this step since no new variables are
+created. \if{html}{\out{<change if role is used>}}}
+
+\item{trained}{A logical to indicate if the quantities for
+preprocessing have been estimated.}
+
+\item{degree}{The polynomial degree to use for smoothing.}
+
+\item{window_size}{The window size to use for smoothing.}
+
+\item{differentiation_order}{An integer for the degree of filtering (zero
+indicates no differentiation).}
+
+\item{skip}{A logical. Should the step be skipped when the
+recipe is baked by \code{\link[=bake]{bake()}}? While all operations are baked
+when \code{\link[=prep]{prep()}} is run, some operations may not be able to be
+conducted on new data (e.g. processing the outcome variable(s)).
+Care should be taken when using \code{skip = TRUE} as it may affect
+the computations for subsequent operations}
+
+\item{id}{A character string that is unique to this step to identify it.}
+}
+\value{
+An updated version of \code{recipe} with the new step added to the
+sequence of any existing operations.
+}
+\description{
+\code{step_measure_savitzky_golay} creates a \emph{specification} of a recipe
+step that \if{html}{\out{<what it does>}}
+}
+\section{Tidying}{
+When you \code{\link[=tidy.recipe]{tidy()}} this step, a tibble with columns
+\if{html}{\out{<describe tidying>}} is returned.
+}
+
diff --git a/tests/testthat/test_savitzky_golay.R b/tests/testthat/test_savitzky_golay.R
new file mode 100644
index 0000000..e69de29

From 65d522714610cfe1e639c27b2f5f399fdcc5df8c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=98topepo=E2=80=99?= <‘mxkuhn@gmail.com’>
Date: Wed, 3 Jan 2024 17:05:40 -0500
Subject: [PATCH 02/13] remove terms, more scaffolding

---
 NAMESPACE                          |  1 +
 R/helpers.R                        | 15 ++++++--
 R/savitzky_golay.R                 | 58 +++++++++++++++++++++---------
 man/step_measure_savitzky_golay.Rd | 20 ++++++-----
 4 files changed, 67 insertions(+), 27 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 732fdf2..ad90683 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -12,6 +12,7 @@ S3method(print,step_baseline)
 S3method(print,step_measure_input_long)
 S3method(print,step_measure_input_wide)
 S3method(print,step_measure_savitzky_golay)
+S3method(required_pkgs,step_isomap)
 S3method(tidy,step_measure_input_long)
 S3method(tidy,step_measure_input_wide)
 S3method(tidy,step_measure_savitzky_golay)
diff --git a/R/helpers.R b/R/helpers.R
index 4945063..0218aa7 100644
--- a/R/helpers.R
+++ b/R/helpers.R
@@ -18,8 +18,6 @@ add_location <- function(.data, loc) {
 
 # Assumes identical locations
 measure_to_matrix <- function(x) {
-  n <- length(x)
-  loc <- x[[1]]$location
   res <- do.call("rbind", purrr::map(x, ~ .x[["value"]]))
   res
 }
@@ -44,7 +42,18 @@ matrix_to_measure <- function(x, loc) {
 
 measure_to_tibble <- function(x) {
   x <-
-    tibble::tibble(x = sg, sample_num = seq_along(x)) %>%
+    tibble::tibble(x = x, sample_num = seq_along(x)) %>%
     tidyr::unnest(cols = x)
   x
 }
+
+# ------------------------------------------------------------------------------
+
+check_for_measure <- function(x) {
+  if (!any(names(x) == ".measures")) {
+    cli::cli_abort("A column called {.code .measures} in the data. See
+                    {.fn step_measure_input_wide} and
+                    {.fn step_measure_input_long}.")
+  }
+  invisible(NULL)
+}
diff --git a/R/savitzky_golay.R b/R/savitzky_golay.R
index c43794c..b2a36d8 100644
--- a/R/savitzky_golay.R
+++ b/R/savitzky_golay.R
@@ -1,16 +1,12 @@
 #' Savitzky-Golay Pre-Processing
 #'
 #' `step_measure_savitzky_golay` creates a *specification* of a recipe
-#'  step that <what it does>
+#'  step that smooths and filters the measurement sequence.
 #'
 #' @param recipe A recipe object. The step will be added to the
 #'  sequence of operations for this recipe.
-#' @param ... One or more selector functions to choose which
-#'  variables are affected by the step. See [selections()]
-#'  for more details. For the `tidy` method, these are not
-#'  currently used.
 #' @param role Not used by this step since no new variables are
-#'  created. <change if role is used>
+#'  created.
 #' @param trained A logical to indicate if the quantities for
 #'  preprocessing have been estimated.
 #' @param degree The polynomial degree to use for smoothing.
@@ -29,6 +25,14 @@
 #'
 #' @export
 #' @details
+#' No selectors should be supplied to this step function. The data should be in
+#' a special internal format produced by [step_measure_input_wide()] or
+#' [step_measure_input_long()].
+#'
+#' Measurements are assumed to be equally spaced.
+#'
+#' The step will produce fewer predictor values (i.e., fewer measurements) than
+#' the input.
 #'
 #' # Tidying
 #'
@@ -39,7 +43,6 @@
 
 step_measure_savitzky_golay <-
     function(recipe,
-             ...,
              role = NA,
              trained = FALSE,
              degree = 3,
@@ -50,7 +53,6 @@ step_measure_savitzky_golay <-
       recipes::add_step(
         recipe,
         step_measure_savitzky_golay_new(
-          terms = enquos(...),
           trained = trained,
           role = role,
           degree = degree,
@@ -63,11 +65,10 @@ step_measure_savitzky_golay <-
     }
 
 step_measure_savitzky_golay_new <-
-  function(terms, role, trained, degree, window_size, differentiation_order,
+  function(role, trained, degree, window_size, differentiation_order,
            na_rm, skip, id) {
     recipes::step(
       subclass = "measure_savitzky_golay",
-      terms = terms,
       role = role,
       trained = trained,
       degree = degree,
@@ -80,11 +81,23 @@ step_measure_savitzky_golay_new <-
 
 #' @export
 prep.step_measure_savitzky_golay <- function(x, training, info = NULL, ...) {
-  col_names <- recipes::recipes_eval_select(x$terms, training, info)
-  recipes::check_type(training[, col_names])
+  check_for_measure(training)
+  if (!is.numeric(x$degree) | length(x$degree) != 1 | x$degree < 1) {
+    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$differentiation_order < 0) {
+    cli::cli_abort("{.arg differentiation_order} to {.fn  step_measure_savitzky_golay} should
+                    be a single integer greater than -1.")
+  }
+  if (!is.numeric(x$window_size) | length(x$window_size) != 1
+      | x$window_size < 1 | x$window_size %% 2 != 1) {
+    cli::cli_abort("{.arg window_size} to {.fn  step_measure_savitzky_golay} should
+                    be a single odd integer greater than 0.")
+  }
 
   step_measure_savitzky_golay_new(
-    terms = x$terms,
     role = x$role,
     trained = TRUE,
     degree = x$degree,
@@ -105,6 +118,7 @@ bake.step_measure_savitzky_golay <- function(object, new_data, ...) {
       degree = object$degree,
       window = object$window_size
     )
+  # TODO try to approximate the wave numbers that were input.
   new_data$.measures <- res
   tibble::as_tibble(new_data)
 }
@@ -113,7 +127,8 @@ bake.step_measure_savitzky_golay <- function(object, new_data, ...) {
 print.step_measure_savitzky_golay <-
   function(x, width = max(20, options()$width - 30), ...) {
     title <- "Savitzky-Golay preprocessing "
-    recipes::print_step(names(x$means), x$terms, x$trained, title, width)
+    recipes::print_step("<internal measurements>", "<internal measurements>",
+                        x$trained, title, width)
     invisible(x)
   }
 
@@ -132,6 +147,13 @@ tidy.step_measure_savitzky_golay <- function(x, ...) {
   res
 }
 
+#' @rdname measure-required_pkgs.recipe
+#' @export
+required_pkgs.step_isomap <- function(x, ...) {
+  c("measure", "prospectr")
+}
+
+
 # ------------------------------------------------------------------------------
 
 .comp_savitzky_golay <- function(dat, diffs = 1, degree = 2, window = 3, ...) {
@@ -149,10 +171,14 @@ tidy.step_measure_savitzky_golay <- function(x, ...) {
       w = window,
       ...
     )
-  res <- rlang::eval_tidy(cl)
+  res <- try(rlang::eval_tidy(cl), silent = TRUE)
+  if (inherits(res, "try-error")) {
+    msg <- as.character(res)
+    cli::cli_abort("Savitzky-Golay computations failed with error: {msg}")
+  }
 
   if (ncol(res) != ncol(dat)) {
-    # Prob can do better
+    # TODO Prob can do better; can we appriximate what the wave numbers should be?
     loc <- 1:ncol(res)
   }
 
diff --git a/man/step_measure_savitzky_golay.Rd b/man/step_measure_savitzky_golay.Rd
index 045e988..89fef6f 100644
--- a/man/step_measure_savitzky_golay.Rd
+++ b/man/step_measure_savitzky_golay.Rd
@@ -6,7 +6,6 @@
 \usage{
 step_measure_savitzky_golay(
   recipe,
-  ...,
   role = NA,
   trained = FALSE,
   degree = 3,
@@ -20,13 +19,8 @@ step_measure_savitzky_golay(
 \item{recipe}{A recipe object. The step will be added to the
 sequence of operations for this recipe.}
 
-\item{...}{One or more selector functions to choose which
-variables are affected by the step. See \code{\link[=selections]{selections()}}
-for more details. For the \code{tidy} method, these are not
-currently used.}
-
 \item{role}{Not used by this step since no new variables are
-created. \if{html}{\out{<change if role is used>}}}
+created.}
 
 \item{trained}{A logical to indicate if the quantities for
 preprocessing have been estimated.}
@@ -53,7 +47,17 @@ sequence of any existing operations.
 }
 \description{
 \code{step_measure_savitzky_golay} creates a \emph{specification} of a recipe
-step that \if{html}{\out{<what it does>}}
+step that smooths and filters the measurement sequence.
+}
+\details{
+No selectors should be supplied to this step function. The data should be in
+a special internal format produced by \code{\link[=step_measure_input_wide]{step_measure_input_wide()}} or
+\code{\link[=step_measure_input_long]{step_measure_input_long()}}.
+
+Measurements are assumed to be equally spaced.
+
+The step will produce fewer predictor values (i.e., fewer measurements) than
+the input.
 }
 \section{Tidying}{
 When you \code{\link[=tidy.recipe]{tidy()}} this step, a tibble with columns

From b7fe7be94c8fe84f88e4151fa0d425c9f1126df6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=98topepo=E2=80=99?= <‘mxkuhn@gmail.com’>
Date: Wed, 3 Jan 2024 21:57:52 -0500
Subject: [PATCH 03/13] small changes

---
 R/savitzky_golay.R                 | 46 +++++++++++++++++++++++-------
 man/step_measure_savitzky_golay.Rd | 33 ++++++++++++++++-----
 2 files changed, 61 insertions(+), 18 deletions(-)

diff --git a/R/savitzky_golay.R b/R/savitzky_golay.R
index b2a36d8..a3dcf76 100644
--- a/R/savitzky_golay.R
+++ b/R/savitzky_golay.R
@@ -9,8 +9,8 @@
 #'  created.
 #' @param trained A logical to indicate if the quantities for
 #'  preprocessing have been estimated.
-#' @param degree The polynomial degree to use for smoothing.
-#' @param window_size The window size to use for smoothing.
+#' @param degree An integer for the polynomial degree to use for smoothing.
+#' @param window_size An odd integer for the window size to use for smoothing.
 #' @param differentiation_order An integer for the degree of filtering (zero
 #' indicates no differentiation).
 #' @param skip A logical. Should the step be skipped when the
@@ -24,22 +24,40 @@
 #' sequence of any existing operations.
 #'
 #' @export
+#' @family measure-smoothing
+#' @family measure-differencing
 #' @details
-#' No selectors should be supplied to this step function. The data should be in
+#' This method can both smooth out random noise and reduce between-predictor
+#' correlation. It fits a polynomial to a window of measurements and this results
+#' in fewer measurements than the input. Measurements are assumed to be equally
+#' spaced.
+#'
+#' The polynomial degree should be less than the window size.
+#'
+#' **No selectors should be supplied to this step function**. The data should be in
 #' a special internal format produced by [step_measure_input_wide()] or
 #' [step_measure_input_long()].
 #'
-#' Measurements are assumed to be equally spaced.
-#'
-#' The step will produce fewer predictor values (i.e., fewer measurements) than
-#' the input.
+#' The measurement locations are reset to integer indices starting at one.
 #'
 #' # Tidying
 #'
 #' When you [`tidy()`][tidy.recipe()] this step, a tibble with columns
 #' <describe tidying> is returned.
 #'
-# @examples
+#' @examples
+#' if (rlang::is_installed("prospectr")) {
+#'   rec <-
+#'     recipe(water + fat + protein ~ ., data = meats_long) %>%
+#'     update_role(id, new_role = "id") %>%
+#'     step_measure_input_long(transmittance, location = vars(channel)) %>%
+#'     step_measure_savitzky_golay(
+#'       differentiation_order = 1,
+#'       degree = 3,
+#'       window_size = 5
+#'     ) %>%
+#'     prep()
+#' }
 
 step_measure_savitzky_golay <-
     function(recipe,
@@ -88,14 +106,20 @@ prep.step_measure_savitzky_golay <- function(x, training, info = NULL, ...) {
   }
   if (!is.numeric(x$differentiation_order) | length(x$differentiation_order) != 1
       | x$differentiation_order < 0) {
-    cli::cli_abort("{.arg differentiation_order} to {.fn  step_measure_savitzky_golay} should
-                    be a single integer greater than -1.")
+    cli::cli_abort("{.arg differentiation_order} to
+                    {.fn  step_measure_savitzky_golay} should be a single \\
+                    integer greater than -1.")
   }
   if (!is.numeric(x$window_size) | length(x$window_size) != 1
       | x$window_size < 1 | x$window_size %% 2 != 1) {
-    cli::cli_abort("{.arg window_size} to {.fn  step_measure_savitzky_golay} should
+    cli::cli_abort("{.arg window_size} to {.fn  step_measure_savitzky_golay} should \\
                     be a single odd integer greater than 0.")
   }
+  if (x$window_size <= x$degree) {
+    cli::cli_abort("The {.arg window_size} value of {x$window_size} for \\
+                    {.fn  step_measure_savitzky_golay} should \\
+                    be greater or equal to the {.arg degree} value of {x$degree}.")
+  }
 
   step_measure_savitzky_golay_new(
     role = x$role,
diff --git a/man/step_measure_savitzky_golay.Rd b/man/step_measure_savitzky_golay.Rd
index 89fef6f..2b40761 100644
--- a/man/step_measure_savitzky_golay.Rd
+++ b/man/step_measure_savitzky_golay.Rd
@@ -25,9 +25,9 @@ created.}
 \item{trained}{A logical to indicate if the quantities for
 preprocessing have been estimated.}
 
-\item{degree}{The polynomial degree to use for smoothing.}
+\item{degree}{An integer for the polynomial degree to use for smoothing.}
 
-\item{window_size}{The window size to use for smoothing.}
+\item{window_size}{An odd integer for the window size to use for smoothing.}
 
 \item{differentiation_order}{An integer for the degree of filtering (zero
 indicates no differentiation).}
@@ -50,17 +50,36 @@ sequence of any existing operations.
 step that smooths and filters the measurement sequence.
 }
 \details{
-No selectors should be supplied to this step function. The data should be in
+This method can both smooth out random noise and reduce between-predictor
+correlation. It fits a polynomial to a window of measurements and this results
+in fewer measurements than the input. Measurements are assumed to be equally
+spaced.
+
+The polynomial degree should be less than the window size.
+
+\strong{No selectors should be supplied to this step function}. The data should be in
 a special internal format produced by \code{\link[=step_measure_input_wide]{step_measure_input_wide()}} or
 \code{\link[=step_measure_input_long]{step_measure_input_long()}}.
 
-Measurements are assumed to be equally spaced.
-
-The step will produce fewer predictor values (i.e., fewer measurements) than
-the input.
+The measurement locations are reset to integer indices starting at one.
 }
 \section{Tidying}{
 When you \code{\link[=tidy.recipe]{tidy()}} this step, a tibble with columns
 \if{html}{\out{<describe tidying>}} is returned.
 }
 
+\examples{
+if (rlang::is_installed("prospectr")) {
+  rec <-
+    recipe(water + fat + protein ~ ., data = meats_long) \%>\%
+    update_role(id, new_role = "id") \%>\%
+    step_measure_input_long(transmittance, location = vars(channel)) \%>\%
+    step_measure_savitzky_golay(
+      differentiation_order = 1,
+      degree = 3,
+      window_size = 5
+    ) \%>\%
+    prep()
+}
+}
+\concept{measure-smoothing}

From 367327e78c8d38b24ee82e269c70aa73ea11f651 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=98topepo=E2=80=99?= <‘mxkuhn@gmail.com’>
Date: Wed, 3 Jan 2024 21:59:12 -0500
Subject: [PATCH 04/13] better error

---
 R/helpers.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/helpers.R b/R/helpers.R
index 0218aa7..48cd0bd 100644
--- a/R/helpers.R
+++ b/R/helpers.R
@@ -51,7 +51,7 @@ measure_to_tibble <- function(x) {
 
 check_for_measure <- function(x) {
   if (!any(names(x) == ".measures")) {
-    cli::cli_abort("A column called {.code .measures} in the data. See
+    cli::cli_abort("A column called {.code .measures} should be in the data. See
                     {.fn step_measure_input_wide} and
                     {.fn step_measure_input_long}.")
   }

From c8afcc4602bca0e085cbe76575f242281fd920cb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=98topepo=E2=80=99?= <‘mxkuhn@gmail.com’>
Date: Thu, 4 Jan 2024 07:14:15 -0500
Subject: [PATCH 05/13] small updates

---
 R/input_wide.R     | 1 +
 R/savitzky_golay.R | 8 ++++----
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/R/input_wide.R b/R/input_wide.R
index cf7cc20..87a2567 100644
--- a/R/input_wide.R
+++ b/R/input_wide.R
@@ -172,6 +172,7 @@ wide_to_list <- function(x, ind, selections) {
     ) %>%
     dplyr::select(-temp) %>%
     # TODO convert some of this to use vctrs
+    # https://www.tidyverse.org/blog/2023/04/performant-packages/#nest
     tidyr::nest(.by = c(-value), .key = ".measures") %>%
     dplyr::select(-..row) %>%
     add_location(ind)
diff --git a/R/savitzky_golay.R b/R/savitzky_golay.R
index a3dcf76..e95d119 100644
--- a/R/savitzky_golay.R
+++ b/R/savitzky_golay.R
@@ -107,17 +107,17 @@ prep.step_measure_savitzky_golay <- function(x, training, info = NULL, ...) {
   if (!is.numeric(x$differentiation_order) | length(x$differentiation_order) != 1
       | x$differentiation_order < 0) {
     cli::cli_abort("{.arg differentiation_order} to
-                    {.fn  step_measure_savitzky_golay} should be a single \\
+                    {.fn  step_measure_savitzky_golay} should be a single
                     integer greater than -1.")
   }
   if (!is.numeric(x$window_size) | length(x$window_size) != 1
       | x$window_size < 1 | x$window_size %% 2 != 1) {
-    cli::cli_abort("{.arg window_size} to {.fn  step_measure_savitzky_golay} should \\
+    cli::cli_abort("{.arg window_size} to {.fn  step_measure_savitzky_golay} should
                     be a single odd integer greater than 0.")
   }
   if (x$window_size <= x$degree) {
-    cli::cli_abort("The {.arg window_size} value of {x$window_size} for \\
-                    {.fn  step_measure_savitzky_golay} should \\
+    cli::cli_abort("The {.arg window_size} value of {x$window_size} for
+                    {.fn  step_measure_savitzky_golay} should
                     be greater or equal to the {.arg degree} value of {x$degree}.")
   }
 

From daa075ff6fa2b4fca53459c6bfa6157f9621f355 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=98topepo=E2=80=99?= <‘mxkuhn@gmail.com’>
Date: Thu, 4 Jan 2024 08:47:15 -0500
Subject: [PATCH 06/13] fail if missing data per sample

---
 R/checks.R                               | 15 +++++++++++++++
 R/input_long.R                           |  2 ++
 tests/testthat/test_measure_input_long.R |  8 +++++---
 3 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/R/checks.R b/R/checks.R
index f8d6bf5..97f4e4c 100644
--- a/R/checks.R
+++ b/R/checks.R
@@ -16,3 +16,18 @@ check_single_selector <- function(res, arg) {
     rlang::abort(msg)
   }
 }
+
+check_measure_dims <- function(x) {
+  num_rows <- purrr::map_int(x$.measures, nrow)
+  num_unique <- sort(table(num_rows), decreasing = TRUE)
+  most_freq <- as.integer(names(num_unique)[1])
+  if (length(num_unique) != 1) {
+    which_rows <- which(num_rows != most_freq)
+    n_bad <- length(which_rows)
+    chr_rows <- paste(which_rows, collapse = ", ")
+    cli::cli_abort("The number of rows in each measure should be the same.
+                   Most samples have {most_freq} rows and these do not:
+                   {chr_rows}. Please pad the input with missing values.")
+  }
+  invisible(NULL)
+}
diff --git a/R/input_long.R b/R/input_long.R
index ebbf917..8f3829c 100644
--- a/R/input_long.R
+++ b/R/input_long.R
@@ -117,6 +117,8 @@ bake.step_measure_input_long <- function(object, new_data, ...) {
       tidyr::nest(.by = c(-value), .key = ".measures")
   }
 
+  check_measure_dims(new_data)
+
   new_data
 }
 
diff --git a/tests/testthat/test_measure_input_long.R b/tests/testthat/test_measure_input_long.R
index b7d3330..1aa20c1 100644
--- a/tests/testthat/test_measure_input_long.R
+++ b/tests/testthat/test_measure_input_long.R
@@ -57,10 +57,12 @@ test_that("ingest long format data", {
 
   ### missing rows
 
-  prep_2 <-
+  expect_snapshot(
     recipe(water + fat + protein ~ ., data = miss_train) %>%
-    step_measure_input_long(absorp, location = vars(ind)) %>%
-    prep()
+      step_measure_input_long(absorp, location = vars(ind)) %>%
+      prep(),
+    error = TRUE
+  )
 
   ## missing values
 

From fa9ef375b9c6411053133bbbb05b74728acf0139 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=98topepo=E2=80=99?= <‘mxkuhn@gmail.com’>
Date: Thu, 4 Jan 2024 08:47:26 -0500
Subject: [PATCH 07/13] re-generate tests and snapshots

---
 DESCRIPTION                                 |   1 +
 R/helpers.R                                 |   1 +
 R/savitzky_golay.R                          |  10 +-
 man/step_measure_savitzky_golay.Rd          |   1 +
 tests/testthat/_snaps/measure_collect.md    | 120 -------
 tests/testthat/_snaps/measure_input_long.md |  22 +-
 tests/testthat/_snaps/measure_input_wide.md |   6 +-
 tests/testthat/_snaps/savitzky_golay.md     | 380 ++++++++++++++++++++
 tests/testthat/test-data-transformations.R  |  10 +
 tests/testthat/test_savitzky_golay.R        | 110 ++++++
 10 files changed, 526 insertions(+), 135 deletions(-)
 delete mode 100644 tests/testthat/_snaps/measure_collect.md
 create mode 100644 tests/testthat/_snaps/savitzky_golay.md
 create mode 100644 tests/testthat/test-data-transformations.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 14e8677..efeadd9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -22,6 +22,7 @@ Suggests:
     covr,
     knitr,
     modeldata,
+    prospectr,
     rmarkdown,
     roxygen2,
     testthat (>= 3.0.0),
diff --git a/R/helpers.R b/R/helpers.R
index 48cd0bd..abaf028 100644
--- a/R/helpers.R
+++ b/R/helpers.R
@@ -18,6 +18,7 @@ add_location <- function(.data, loc) {
 
 # Assumes identical locations
 measure_to_matrix <- function(x) {
+  # silently recycles :-O
   res <- do.call("rbind", purrr::map(x, ~ .x[["value"]]))
   res
 }
diff --git a/R/savitzky_golay.R b/R/savitzky_golay.R
index e95d119..d8c4bdc 100644
--- a/R/savitzky_golay.R
+++ b/R/savitzky_golay.R
@@ -115,11 +115,6 @@ prep.step_measure_savitzky_golay <- function(x, training, info = NULL, ...) {
     cli::cli_abort("{.arg window_size} to {.fn  step_measure_savitzky_golay} should
                     be a single odd integer greater than 0.")
   }
-  if (x$window_size <= x$degree) {
-    cli::cli_abort("The {.arg window_size} value of {x$window_size} for
-                    {.fn  step_measure_savitzky_golay} should
-                    be greater or equal to the {.arg degree} value of {x$degree}.")
-  }
 
   step_measure_savitzky_golay_new(
     role = x$role,
@@ -196,13 +191,16 @@ required_pkgs.step_isomap <- function(x, ...) {
       ...
     )
   res <- try(rlang::eval_tidy(cl), silent = TRUE)
+
   if (inherits(res, "try-error")) {
     msg <- as.character(res)
+    msg <- strsplit(msg, " : ")[[1]][2]
+    msg <- gsub("\\n", "", msg)
     cli::cli_abort("Savitzky-Golay computations failed with error: {msg}")
   }
 
   if (ncol(res) != ncol(dat)) {
-    # TODO Prob can do better; can we appriximate what the wave numbers should be?
+    # TODO Prob can do better; can we approximate what the wave numbers should be?
     loc <- 1:ncol(res)
   }
 
diff --git a/man/step_measure_savitzky_golay.Rd b/man/step_measure_savitzky_golay.Rd
index 2b40761..42bdc8f 100644
--- a/man/step_measure_savitzky_golay.Rd
+++ b/man/step_measure_savitzky_golay.Rd
@@ -82,4 +82,5 @@ if (rlang::is_installed("prospectr")) {
     prep()
 }
 }
+\concept{measure-differencing}
 \concept{measure-smoothing}
diff --git a/tests/testthat/_snaps/measure_collect.md b/tests/testthat/_snaps/measure_collect.md
deleted file mode 100644
index 518b671..0000000
--- a/tests/testthat/_snaps/measure_collect.md
+++ /dev/null
@@ -1,120 +0,0 @@
-# Print recipe with step_measure_collect works
-
-    Code
-      meats_rec
-    Message <cliMessage>
-      
-      -- Recipe ----------------------------------------------------------------------
-      
-      -- Inputs 
-      Number of variables by role
-      descriptor:        3
-      undeclared role: 100
-      
-      -- Operations 
-      * Collect measurements: starts_with("x_")
-
----
-
-    Code
-      meats_long_rec
-    Message <cliMessage>
-      
-      -- Recipe ----------------------------------------------------------------------
-      
-      -- Inputs 
-      Number of variables by role
-      descriptor:      4
-      undeclared role: 2
-      
-      -- Operations 
-      * Collect measurements: channel, transmittance
-
-# Prep recipe with step_measure_collect works
-
-    Code
-      meats_prep
-    Message <cliMessage>
-      
-      -- Recipe ----------------------------------------------------------------------
-      
-      -- Inputs 
-      Number of variables by role
-      descriptor:        3
-      undeclared role: 100
-      
-      -- Training information 
-      Training data contained 215 data points and no incomplete rows.
-      
-      -- Operations 
-      * Collect measurements: x_001, x_002, x_003, x_004, x_005, x_006, ... | Trained
-
----
-
-    Code
-      meats_long_prep
-    Message <cliMessage>
-      
-      -- Recipe ----------------------------------------------------------------------
-      
-      -- Inputs 
-      Number of variables by role
-      descriptor:      4
-      undeclared role: 2
-      
-      -- Training information 
-      Training data contained 21500 data points and no incomplete rows.
-      
-      -- Operations 
-      * Collect measurements: channel, transmittance | Trained
-
-# Bake recipe with step_measure_collect works
-
-    Code
-      meats_bake
-    Output
-      # A tibble: 215 x 2
-         .index          .measures
-          <int> <list<tibble[,5]>>
-       1      1          [100 x 5]
-       2      2          [100 x 5]
-       3      3          [100 x 5]
-       4      4          [100 x 5]
-       5      5          [100 x 5]
-       6      6          [100 x 5]
-       7      7          [100 x 5]
-       8      8          [100 x 5]
-       9      9          [100 x 5]
-      10     10          [100 x 5]
-      # i 205 more rows
-
----
-
-    Code
-      meats_long_bake
-    Output
-      # A tibble: 1 x 2
-        .index .measures            
-         <int> <list>               
-      1      1 <tibble [21,500 x 6]>
-
-# Tidy recipe with step_measure_collect works
-
-    Code
-      tidy(meats_rec)
-    Output
-      # A tibble: 1 x 6
-        number operation type            trained skip  id                   
-         <int> <chr>     <chr>           <lgl>   <lgl> <chr>                
-      1      1 step      measure_collect FALSE   FALSE measure_collect_Bp5vK
-
----
-
-    Code
-      tidy(meats_long_rec)
-    Output
-      # A tibble: 1 x 6
-        number operation type            trained skip  id                   
-         <int> <chr>     <chr>           <lgl>   <lgl> <chr>                
-      1      1 step      measure_collect FALSE   FALSE measure_collect_RUieL
-
diff --git a/tests/testthat/_snaps/measure_input_long.md b/tests/testthat/_snaps/measure_input_long.md
index 6ad90b0..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 ----------------------------------------------------------------------
       
@@ -56,7 +56,7 @@
       Training data contained 20000 data points and no incomplete rows.
       
       -- Operations 
-      * Collate long analytical measurements: absorp, ind | Trained
+      * Collate long analytical measurements: absorp and ind | Trained
 
 ---
 
@@ -87,17 +87,27 @@
     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
 
+---
+
+    Code
+      recipe(water + fat + protein ~ ., data = miss_train) %>%
+        step_measure_input_long(absorp, location = vars(ind)) %>% prep()
+    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.
+
 ---
 
     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).
@@ -107,7 +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/savitzky_golay.md b/tests/testthat/_snaps/savitzky_golay.md
new file mode 100644
index 0000000..73308c9
--- /dev/null
+++ b/tests/testthat/_snaps/savitzky_golay.md
@@ -0,0 +1,380 @@
+# savitzky-golay inputs
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `.comp_savitzky_golay()`:
+      ! Savitzky-Golay computations failed with error: polynomial order p must be geater or equal to differentiation order m
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `.comp_savitzky_golay()`:
+      ! Savitzky-Golay computations failed with error: polynomial order p must be geater or equal to differentiation order m
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `.comp_savitzky_golay()`:
+      ! Savitzky-Golay computations failed with error: polynomial order p must be geater or equal to differentiation order m
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `.comp_savitzky_golay()`:
+      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `.comp_savitzky_golay()`:
+      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `.comp_savitzky_golay()`:
+      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `.comp_savitzky_golay()`:
+      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `.comp_savitzky_golay()`:
+      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `.comp_savitzky_golay()`:
+      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `.comp_savitzky_golay()`:
+      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `.comp_savitzky_golay()`:
+      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `prep()`:
+      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `.comp_savitzky_golay()`:
+      ! Savitzky-Golay computations failed with error: polynomial order p must be geater or equal to differentiation order m
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `.comp_savitzky_golay()`:
+      ! Savitzky-Golay computations failed with error: polynomial order p must be geater or equal to differentiation order m
+
+---
+
+    Code
+      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
+      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
+    Condition
+      Error in `step_measure_savitzky_golay()`:
+      Caused by error in `.comp_savitzky_golay()`:
+      ! Savitzky-Golay computations failed with error: polynomial order p must be geater or equal to differentiation order m
+
diff --git a/tests/testthat/test-data-transformations.R b/tests/testthat/test-data-transformations.R
new file mode 100644
index 0000000..e645356
--- /dev/null
+++ b/tests/testthat/test-data-transformations.R
@@ -0,0 +1,10 @@
+test_that("transform measure to matrix", {
+  rec <-
+    recipe(water + fat + protein ~ ., data = meats_long) %>%
+    update_role(id, new_role = "id") %>%
+    step_measure_input_long(transmittance, location = vars(channel)) %>%
+    prep()
+
+  spect_start <- measure:::measure_to_matrix(rec$template$.measures)
+
+})
diff --git a/tests/testthat/test_savitzky_golay.R b/tests/testthat/test_savitzky_golay.R
index e69de29..91104df 100644
--- a/tests/testthat/test_savitzky_golay.R
+++ b/tests/testthat/test_savitzky_golay.R
@@ -0,0 +1,110 @@
+test_that("savitzky-golay computations", {
+  skip_if_not_installed("prospectr")
+
+  # ------------------------------------------------------------------------------
+
+  rec <-
+    recipe(water + fat + protein ~ ., data = meats_long) %>%
+    update_role(id, new_role = "id") %>%
+    step_measure_input_long(transmittance, location = vars(channel)) %>%
+    prep()
+
+  spect_start <- measure:::measure_to_matrix(rec$template$.measures)
+
+  # ------------------------------------------------------------------------------
+
+  grid <- expand.grid(diffs = 0:3, deg = 4:6, wn = c(15, 21, 25))
+
+  for (i in 1:nrow(grid)) {
+    meas_res <-
+      measure:::.comp_savitzky_golay(
+        rec$template$.measures,
+        diffs = grid$diffs[i],
+        degree = grid$deg[i],
+        window = grid$wn[i]
+      ) %>%
+      measure:::measure_to_matrix()
+    prosp_res <-
+      prospectr::savitzkyGolay(spect_start,
+                               m = grid$diffs[i],
+                               p = grid$deg[i],
+                               w = grid$wn[i])
+    expect_equal(meas_res, prosp_res)
+  }
+
+})
+
+test_that("savitzky-golay inputs", {
+  skip_if_not_installed("prospectr")
+
+  # ------------------------------------------------------------------------------
+
+  rec <-
+    recipe(water + fat + protein ~ ., data = meats_long) %>%
+    update_role(id, new_role = "id") %>%
+    step_measure_input_long(transmittance, location = vars(channel)) %>%
+    prep()
+
+  # ------------------------------------------------------------------------------
+
+  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
+    )
+
+  lst <- NULL
+  for (i in 1:nrow(bad_inputs)) {
+
+    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
+    )
+  }
+
+})
+

From d6bcf0c5e774a850270c7ca07bd03bc1d5125e31 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=98topepo=E2=80=99?= <‘mxkuhn@gmail.com’>
Date: Thu, 4 Jan 2024 09:11:11 -0500
Subject: [PATCH 08/13] clean up some documentation

---
 R/helpers.R                                |  6 +--
 R/input_long.R                             |  9 ++++
 R/savitzky_golay.R                         |  6 ++-
 man/required_pkgs.recipe.Rd                | 15 ++++++
 man/step_measure_input_long.Rd             |  7 +++
 man/tidy.recipe.Rd                         | 21 +++++++++
 tests/testthat/test-data-transformations.R | 53 +++++++++++++++++++++-
 7 files changed, 111 insertions(+), 6 deletions(-)
 create mode 100644 man/required_pkgs.recipe.Rd
 create mode 100644 man/tidy.recipe.Rd

diff --git a/R/helpers.R b/R/helpers.R
index abaf028..72a0158 100644
--- a/R/helpers.R
+++ b/R/helpers.R
@@ -15,10 +15,10 @@ add_location <- function(.data, loc) {
 
 # ------------------------------------------------------------------------------
 # Move between lists of tibbles and matrices (and back)
+# Assumes identical locations. We have code to check that the per-sample
+# dimensions are equal but nothing yet for identical locations.
 
-# Assumes identical locations
 measure_to_matrix <- function(x) {
-  # silently recycles :-O
   res <- do.call("rbind", purrr::map(x, ~ .x[["value"]]))
   res
 }
@@ -37,7 +37,7 @@ matrix_to_measure <- function(x, loc) {
   x <- t(x)
   x <-  tibble::as_tibble(x, .name_repair = "minimal")
 
-  res <- purrr::map(x, ~ tibble::new_tibble(list(value = .x, location = loc)))
+  res <- purrr::map(x, ~ tibble::new_tibble(list(location = loc, value = .x)))
   unname(res)
 }
 
diff --git a/R/input_long.R b/R/input_long.R
index 8f3829c..c7cd75b 100644
--- a/R/input_long.R
+++ b/R/input_long.R
@@ -30,6 +30,13 @@
 #' rows. We advise having a column with 7 unique values indicating which of the
 #' rows correspond to each sample.
 #'
+#' # Missing Data
+#'
+#' Currently, \pkg{measure} assumes that there are equal numbers of values
+#' within a sample. If there are missing values in the measurements, you'll
+#' need to pad them with missing values (as opposed to an absent row in the
+#' long format). If not, an error will occur.
+#'
 #' # Tidying
 #'
 #' When you [`tidy()`][tidy.recipe()] this step, a tibble indicating which of
@@ -130,6 +137,8 @@ print.step_measure_input_long <-
     invisible(x)
   }
 
+#' Tidiers for measure steps
+#' @param x A recipe step.
 #' @rdname tidy.recipe
 #' @export
 tidy.step_measure_input_long <- function(x, ...) {
diff --git a/R/savitzky_golay.R b/R/savitzky_golay.R
index d8c4bdc..6c710aa 100644
--- a/R/savitzky_golay.R
+++ b/R/savitzky_golay.R
@@ -151,7 +151,7 @@ print.step_measure_savitzky_golay <-
     invisible(x)
   }
 
-#' @rdname measure-tidy.recipe
+#' @rdname tidy.recipe
 #' @export
 tidy.step_measure_savitzky_golay <- function(x, ...) {
   if (is_trained(x)) {
@@ -166,7 +166,9 @@ tidy.step_measure_savitzky_golay <- function(x, ...) {
   res
 }
 
-#' @rdname measure-required_pkgs.recipe
+#' Set package dependencies
+#' @param x A step object.
+#' @name required_pkgs.recipe
 #' @export
 required_pkgs.step_isomap <- function(x, ...) {
   c("measure", "prospectr")
diff --git a/man/required_pkgs.recipe.Rd b/man/required_pkgs.recipe.Rd
new file mode 100644
index 0000000..75c46e7
--- /dev/null
+++ b/man/required_pkgs.recipe.Rd
@@ -0,0 +1,15 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/savitzky_golay.R
+\name{required_pkgs.recipe}
+\alias{required_pkgs.recipe}
+\alias{required_pkgs.step_isomap}
+\title{Set package dependencies}
+\usage{
+\method{required_pkgs}{step_isomap}(x, ...)
+}
+\arguments{
+\item{x}{A step object.}
+}
+\description{
+Set package dependencies
+}
diff --git a/man/step_measure_input_long.Rd b/man/step_measure_input_long.Rd
index 2185aa3..37c4e9b 100644
--- a/man/step_measure_input_long.Rd
+++ b/man/step_measure_input_long.Rd
@@ -68,6 +68,13 @@ measure and 7 samples, the input data (in long format) should have 1,400
 rows. We advise having a column with 7 unique values indicating which of the
 rows correspond to each sample.
 }
+\section{Missing Data}{
+Currently, \pkg{measure} assumes that there are equal numbers of values
+within a sample. If there are missing values in the measurements, you'll
+need to pad them with missing values (as opposed to an absent row in the
+long format). If not, an error will occur.
+}
+
 \section{Tidying}{
 When you \code{\link[=tidy.recipe]{tidy()}} this step, a tibble indicating which of
 the original columns were used to reformat the data.
diff --git a/man/tidy.recipe.Rd b/man/tidy.recipe.Rd
new file mode 100644
index 0000000..9efaf39
--- /dev/null
+++ b/man/tidy.recipe.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/input_long.R, R/input_wide.R,
+%   R/savitzky_golay.R
+\name{tidy.step_measure_input_long}
+\alias{tidy.step_measure_input_long}
+\alias{tidy.step_measure_input_wide}
+\alias{tidy.step_measure_savitzky_golay}
+\title{Tidiers for measure steps}
+\usage{
+\method{tidy}{step_measure_input_long}(x, ...)
+
+\method{tidy}{step_measure_input_wide}(x, ...)
+
+\method{tidy}{step_measure_savitzky_golay}(x, ...)
+}
+\arguments{
+\item{x}{A recipe step.}
+}
+\description{
+Tidiers for measure steps
+}
diff --git a/tests/testthat/test-data-transformations.R b/tests/testthat/test-data-transformations.R
index e645356..6ff2a6c 100644
--- a/tests/testthat/test-data-transformations.R
+++ b/tests/testthat/test-data-transformations.R
@@ -1,10 +1,61 @@
 test_that("transform measure to matrix", {
+
+  rec <-
+    recipe(water + fat + protein ~ ., data = meats_long) %>%
+    update_role(id, new_role = "id") %>%
+    step_measure_input_long(transmittance, location = vars(channel)) %>%
+    prep()
+
+  spect_mat <- measure:::measure_to_matrix(rec$template$.measures)
+
+  expect_equal(nrow(spect_mat), length(unique(meats_long$id)))
+  expect_equal(ncol(spect_mat), length(unique(meats_long$channel)))
+
+  ids <- unique(meats_long$id)
+  for (i in seq_along(ids)) {
+    expect_equal(
+      spect_mat[i, ],
+      meats_long[meats_long$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") %>%
     step_measure_input_long(transmittance, location = vars(channel)) %>%
     prep()
 
-  spect_start <- measure:::measure_to_matrix(rec$template$.measures)
+  spect_mat <- measure:::measure_to_matrix(rec$template$.measures)
+
+  locs <- unique(meats_long$channel)
+
+  spect_list <- measure:::matrix_to_measure(spect_mat, locs)
+
+  for (i in seq_along(spect_list)) {
+    expect_equal(
+      spect_list[[i]],
+      rec$template$.measures[[i]]
+    )
+  }
+
+})
+
+test_that("transform tidy format", {
+
+  rec <-
+    recipe(water + fat + protein ~ ., data = meats_long) %>%
+    update_role(id, new_role = "id") %>%
+    step_measure_input_long(transmittance, location = vars(channel)) %>%
+    prep()
+
+  spect_df <- measure:::measure_to_tibble(rec$template$.measures)
+  exp_df <- meats_long[, c("channel", "transmittance", "id")]
+  names(exp_df) <- c("location", "value", "sample_num")
+
+  expect_equal(spect_df, exp_df)
 
 })

From 51c57ec98fa6874a61d06f7aa485cf4b6a67a88f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=98topepo=E2=80=99?= <‘mxkuhn@gmail.com’>
Date: Sat, 6 Jan 2024 17:47:56 -0500
Subject: [PATCH 09/13] adjust inputs if needed

---
 R/savitzky_golay.R                      |  32 ++++-
 man/step_measure_savitzky_golay.Rd      |   5 +-
 tests/testthat/_snaps/savitzky_golay.md | 160 ++++++------------------
 tests/testthat/test_savitzky_golay.R    |  36 ++++--
 4 files changed, 94 insertions(+), 139 deletions(-)

diff --git a/R/savitzky_golay.R b/R/savitzky_golay.R
index 6c710aa..d63f0da 100644
--- a/R/savitzky_golay.R
+++ b/R/savitzky_golay.R
@@ -32,7 +32,10 @@
 #' in fewer measurements than the input. Measurements are assumed to be equally
 #' spaced.
 #'
-#' The polynomial degree should be less than the window size.
+#' The polynomial degree should be less than the window size. Also, window
+#' size must be greater than polynomial degree. If either case is true, the
+#' original argument values are increased to satisfy these conditions (with a
+#' warning).
 #'
 #' **No selectors should be supplied to this step function**. The data should be in
 #' a special internal format produced by [step_measure_input_wide()] or
@@ -106,14 +109,35 @@ prep.step_measure_savitzky_golay <- function(x, training, info = NULL, ...) {
   }
   if (!is.numeric(x$differentiation_order) | length(x$differentiation_order) != 1
       | x$differentiation_order < 0) {
-    cli::cli_abort("{.arg differentiation_order} to
+    cli::cli_abort("The {.arg differentiation_order} argument to
                     {.fn  step_measure_savitzky_golay} should be a single
                     integer greater than -1.")
   }
   if (!is.numeric(x$window_size) | length(x$window_size) != 1
       | x$window_size < 1 | x$window_size %% 2 != 1) {
-    cli::cli_abort("{.arg window_size} to {.fn  step_measure_savitzky_golay} should
-                    be a single odd integer greater than 0.")
+    cli::cli_abort("The {.arg window_size} argument to
+                    {.fn  step_measure_savitzky_golay} should be a single odd
+                    integer greater than 0.")
+  }
+
+  # polynomial order p must be geater or equal to differentiation order m
+  if (x$degree <= x$differentiation_order) {
+    x$degree <- x$differentiation_order + 1
+    cli::cli_warn("The {.arg degree} argument to
+                   {.fn step_measure_savitzky_golay} should be greater than or
+                   equal to {.arg differentiation_order}. The polynomial degree
+                   was increased to {x$degree}.")
+  }
+  # 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$window_size + 1
+     }
+    cli::cli_warn("The {.arg window_size} argument to
+                   {.fn step_measure_savitzky_golay} should be greater than or
+                   equal to {.arg degree}. The polynomial degree was increased
+                   to {x$window_size}.")
   }
 
   step_measure_savitzky_golay_new(
diff --git a/man/step_measure_savitzky_golay.Rd b/man/step_measure_savitzky_golay.Rd
index 42bdc8f..b84bb0a 100644
--- a/man/step_measure_savitzky_golay.Rd
+++ b/man/step_measure_savitzky_golay.Rd
@@ -55,7 +55,10 @@ correlation. It fits a polynomial to a window of measurements and this results
 in fewer measurements than the input. Measurements are assumed to be equally
 spaced.
 
-The polynomial degree should be less than the window size.
+The polynomial degree should be less than the window size. Also, window
+size must be greater than polynomial degree. If either case is true, the
+original argument values are increased to satisfy these conditions (with a
+warning).
 
 \strong{No selectors should be supplied to this step function}. The data should be in
 a special internal format produced by \code{\link[=step_measure_input_wide]{step_measure_input_wide()}} or
diff --git a/tests/testthat/_snaps/savitzky_golay.md b/tests/testthat/_snaps/savitzky_golay.md
index 73308c9..b664c7c 100644
--- a/tests/testthat/_snaps/savitzky_golay.md
+++ b/tests/testthat/_snaps/savitzky_golay.md
@@ -1,112 +1,46 @@
 # savitzky-golay inputs
 
-    Code
-      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
-      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
-      Error in `step_measure_savitzky_golay()`:
-      Caused by error in `.comp_savitzky_golay()`:
-      ! Savitzky-Golay computations failed with error: polynomial order p must be geater or equal to differentiation order m
+    The `degree` argument to `step_measure_savitzky_golay()` should be greater than or equal to `differentiation_order`. The polynomial degree was increased to 3.
 
 ---
 
-    Code
-      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
-      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
-      Error in `step_measure_savitzky_golay()`:
-      Caused by error in `.comp_savitzky_golay()`:
-      ! Savitzky-Golay computations failed with error: polynomial order p must be geater or equal to differentiation order m
+    The `degree` argument to `step_measure_savitzky_golay()` should be greater than or equal to `differentiation_order`. The polynomial degree was increased to 4.
 
 ---
 
-    Code
-      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
-      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
-      Error in `step_measure_savitzky_golay()`:
-      Caused by error in `.comp_savitzky_golay()`:
-      ! Savitzky-Golay computations failed with error: polynomial order p must be geater or equal to differentiation order m
+    The `degree` argument to `step_measure_savitzky_golay()` should be greater than or equal to `differentiation_order`. The polynomial degree was increased to 4.
 
 ---
 
-    Code
-      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
-      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
-      Error in `step_measure_savitzky_golay()`:
-      Caused by error in `.comp_savitzky_golay()`:
-      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+    The `window_size` argument to `step_measure_savitzky_golay()` should be greater than or equal to `degree`. The polynomial degree was increased to 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()
-    Condition
-      Error in `step_measure_savitzky_golay()`:
-      Caused by error in `.comp_savitzky_golay()`:
-      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+    The `window_size` argument to `step_measure_savitzky_golay()` should be greater than or equal to `degree`. The polynomial degree was increased to 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()
-    Condition
-      Error in `step_measure_savitzky_golay()`:
-      Caused by error in `.comp_savitzky_golay()`:
-      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+    The `window_size` argument to `step_measure_savitzky_golay()` should be greater than or equal to `degree`. The polynomial degree was increased to 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()
-    Condition
-      Error in `step_measure_savitzky_golay()`:
-      Caused by error in `.comp_savitzky_golay()`:
-      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+    The `window_size` argument to `step_measure_savitzky_golay()` should be greater than or equal to `degree`. The polynomial degree was increased to 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()
-    Condition
-      Error in `step_measure_savitzky_golay()`:
-      Caused by error in `.comp_savitzky_golay()`:
-      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+    The `window_size` argument to `step_measure_savitzky_golay()` should be greater than or equal to `degree`. The polynomial degree was increased to 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()
-    Condition
-      Error in `step_measure_savitzky_golay()`:
-      Caused by error in `.comp_savitzky_golay()`:
-      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+    The `window_size` argument to `step_measure_savitzky_golay()` should be greater than or equal to `degree`. The polynomial degree was increased to 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()
-    Condition
-      Error in `step_measure_savitzky_golay()`:
-      Caused by error in `.comp_savitzky_golay()`:
-      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+    The `window_size` argument to `step_measure_savitzky_golay()` should be greater than or equal to `degree`. The polynomial degree was increased to 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()
-    Condition
-      Error in `step_measure_savitzky_golay()`:
-      Caused by error in `.comp_savitzky_golay()`:
-      ! Savitzky-Golay computations failed with error: filter length w mus be greater than polynomial order p
+    The `window_size` argument to `step_measure_savitzky_golay()` should be greater than or equal to `degree`. The polynomial degree was increased to 7.
 
 ---
 
@@ -116,7 +50,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -126,7 +60,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -136,7 +70,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -146,7 +80,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -156,7 +90,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -166,7 +100,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -176,7 +110,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -186,7 +120,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -196,7 +130,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -206,7 +140,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -216,7 +150,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -226,7 +160,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -236,7 +170,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -246,7 +180,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -256,7 +190,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -266,7 +200,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -276,7 +210,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -286,7 +220,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -296,7 +230,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -306,7 +240,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -316,7 +250,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -326,7 +260,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -336,7 +270,7 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
@@ -346,35 +280,17 @@
     Condition
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
-      ! `window_size` to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
+      ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
 
 ---
 
-    Code
-      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
-      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
-      Error in `step_measure_savitzky_golay()`:
-      Caused by error in `.comp_savitzky_golay()`:
-      ! Savitzky-Golay computations failed with error: polynomial order p must be geater or equal to differentiation order m
+    The `degree` argument to `step_measure_savitzky_golay()` should be greater than or equal to `differentiation_order`. The polynomial degree was increased to 3.
 
 ---
 
-    Code
-      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
-      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
-      Error in `step_measure_savitzky_golay()`:
-      Caused by error in `.comp_savitzky_golay()`:
-      ! Savitzky-Golay computations failed with error: polynomial order p must be geater or equal to differentiation order m
+    The `degree` argument to `step_measure_savitzky_golay()` should be greater than or equal to `differentiation_order`. The polynomial degree was increased to 4.
 
 ---
 
-    Code
-      rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
-      window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
-      Error in `step_measure_savitzky_golay()`:
-      Caused by error in `.comp_savitzky_golay()`:
-      ! Savitzky-Golay computations failed with error: polynomial order p must be geater or equal to differentiation order m
+    The `degree` argument to `step_measure_savitzky_golay()` should be greater than or equal to `differentiation_order`. The polynomial degree was increased to 4.
 
diff --git a/tests/testthat/test_savitzky_golay.R b/tests/testthat/test_savitzky_golay.R
index 91104df..eaf6a11 100644
--- a/tests/testthat/test_savitzky_golay.R
+++ b/tests/testthat/test_savitzky_golay.R
@@ -90,20 +90,32 @@ test_that("savitzky-golay inputs", {
       3L,   2L,  15
     )
 
-  lst <- NULL
   for (i in 1:nrow(bad_inputs)) {
 
-    expect_snapshot({
-      rec %>%
-        step_measure_savitzky_golay(
-          differentiation_order = bad_inputs$diffs[i],
-          window_size = bad_inputs$wn[i],
-          degree = bad_inputs$deg[i]
-        ) %>%
-        prep()
-    },
-    error = TRUE
-    )
+    if (bad_inputs$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$deg[i]
+          ) %>%
+          prep()
+      },
+      error = TRUE)
+
+    } else {
+      expect_snapshot_warning({
+        rec %>%
+          step_measure_savitzky_golay(
+            differentiation_order = bad_inputs$diffs[i],
+            window_size = bad_inputs$wn[i],
+            degree = bad_inputs$deg[i]
+          ) %>%
+          prep()
+      })
+    }
+
   }
 
 })

From e9af9156b417a2b1b40027f2f41c3396412be392 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=98topepo=E2=80=99?= <‘mxkuhn@gmail.com’>
Date: Sat, 6 Jan 2024 22:03:18 -0500
Subject: [PATCH 10/13] missing arg docs

---
 R/savitzky_golay.R          | 3 +++
 man/required_pkgs.recipe.Rd | 2 ++
 man/tidy.recipe.Rd          | 4 +++-
 3 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/R/savitzky_golay.R b/R/savitzky_golay.R
index d63f0da..65e475b 100644
--- a/R/savitzky_golay.R
+++ b/R/savitzky_golay.R
@@ -176,6 +176,8 @@ print.step_measure_savitzky_golay <-
   }
 
 #' @rdname tidy.recipe
+#' @param x A step object.
+#' @param ... Not used.
 #' @export
 tidy.step_measure_savitzky_golay <- function(x, ...) {
   if (is_trained(x)) {
@@ -192,6 +194,7 @@ tidy.step_measure_savitzky_golay <- function(x, ...) {
 
 #' Set package dependencies
 #' @param x A step object.
+#' @param ... Not used.
 #' @name required_pkgs.recipe
 #' @export
 required_pkgs.step_isomap <- function(x, ...) {
diff --git a/man/required_pkgs.recipe.Rd b/man/required_pkgs.recipe.Rd
index 75c46e7..be5122e 100644
--- a/man/required_pkgs.recipe.Rd
+++ b/man/required_pkgs.recipe.Rd
@@ -9,6 +9,8 @@
 }
 \arguments{
 \item{x}{A step object.}
+
+\item{...}{Not used.}
 }
 \description{
 Set package dependencies
diff --git a/man/tidy.recipe.Rd b/man/tidy.recipe.Rd
index 9efaf39..1c016b2 100644
--- a/man/tidy.recipe.Rd
+++ b/man/tidy.recipe.Rd
@@ -14,7 +14,9 @@
 \method{tidy}{step_measure_savitzky_golay}(x, ...)
 }
 \arguments{
-\item{x}{A recipe step.}
+\item{x}{A step object.}
+
+\item{...}{Not used.}
 }
 \description{
 Tidiers for measure steps

From 740f225944f26cc76b9e75d771fdec0359d3494a Mon Sep 17 00:00:00 2001
From: James Wade <github@jameshwade.com>
Date: Mon, 8 Jan 2024 12:47:34 -0500
Subject: [PATCH 11/13] update test snapshots

---
 tests/testthat/_snaps/measure_input_long.md | 12 +++---
 tests/testthat/_snaps/measure_input_wide.md |  6 +--
 tests/testthat/_snaps/savitzky_golay.md     | 48 ++++++++++-----------
 3 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/tests/testthat/_snaps/measure_input_long.md b/tests/testthat/_snaps/measure_input_long.md
index e115358..3e1f939 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
+    Message <cliMessage>
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -43,7 +43,7 @@
 
     Code
       print(prep_1)
-    Message
+    Message <cliMessage>
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -87,7 +87,7 @@
     Code
       recipe(water + fat + protein ~ absorp, data = na_train) %>%
         step_measure_input_long(absorp) %>% prep()
-    Condition
+    Error <recipes_error_step>
       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()
-    Condition
+    Error <recipes_error_step>
       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()
-    Condition
+    Error <recipes_error_step>
       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()
-    Condition
+    Error <recipes_error_step>
       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 98d5e98..5c84336 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
+    Message <cliMessage>
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -48,7 +48,7 @@
 
     Code
       print(prep_1)
-    Message
+    Message <cliMessage>
       
       -- 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()
-    Condition
+    Error <recipes_error_step>
       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/savitzky_golay.md b/tests/testthat/_snaps/savitzky_golay.md
index b664c7c..cf647a4 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$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -57,7 +57,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       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$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -77,7 +77,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       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$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -97,7 +97,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       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$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -117,7 +117,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       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$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -137,7 +137,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       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$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -157,7 +157,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       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$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -177,7 +177,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       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$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -197,7 +197,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       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$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -217,7 +217,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       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$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -237,7 +237,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       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$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -257,7 +257,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       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$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       Error in `step_measure_savitzky_golay()`:
       Caused by error in `prep()`:
       ! The `window_size` argument to `step_measure_savitzky_golay()` should be a single odd integer greater than 0.
@@ -277,7 +277,7 @@
     Code
       rec %>% step_measure_savitzky_golay(differentiation_order = bad_inputs$diffs[i],
       window_size = bad_inputs$wn[i], degree = bad_inputs$deg[i]) %>% prep()
-    Condition
+    Error <recipes_error_step>
       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.

From a96d42c01b1d0d39838ef67680652d2ecee1786d Mon Sep 17 00:00:00 2001
From: James Wade <github@jameshwade.com>
Date: Mon, 8 Jan 2024 13:21:49 -0500
Subject: [PATCH 12/13] update snapshops, cleanup description and namespace

---
 DESCRIPTION                                  |  5 -----
 NAMESPACE                                    | 10 ++++++++++
 R/helpers.R                                  | 21 +++++++++++++++++++-
 man/tidy.recipe.Rd                           | 10 ++++++++--
 tests/testthat/_snaps/measure_input_long.md  | 10 +++++-----
 tests/testthat/_snaps/measure_input_wide.md  |  6 +++---
 tests/testthat/_snaps/measure_output_long.md | 16 +++------------
 7 files changed, 49 insertions(+), 29 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f36d4c2..fc96346 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -40,8 +40,3 @@ Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3.9000
-VignetteBuilder: knitr
-Depends: 
-    R (>= 3.5.0),
-    recipes
-LazyData: true
\ No newline at end of file
diff --git a/NAMESPACE b/NAMESPACE
index ad90683..0b98d43 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -3,21 +3,31 @@
 S3method(bake,step_baseline)
 S3method(bake,step_measure_input_long)
 S3method(bake,step_measure_input_wide)
+S3method(bake,step_measure_output_long)
+S3method(bake,step_measure_output_wide)
 S3method(bake,step_measure_savitzky_golay)
 S3method(prep,step_baseline)
 S3method(prep,step_measure_input_long)
 S3method(prep,step_measure_input_wide)
+S3method(prep,step_measure_output_long)
+S3method(prep,step_measure_output_wide)
 S3method(prep,step_measure_savitzky_golay)
 S3method(print,step_baseline)
 S3method(print,step_measure_input_long)
 S3method(print,step_measure_input_wide)
+S3method(print,step_measure_output_long)
+S3method(print,step_measure_output_wide)
 S3method(print,step_measure_savitzky_golay)
 S3method(required_pkgs,step_isomap)
 S3method(tidy,step_measure_input_long)
 S3method(tidy,step_measure_input_wide)
+S3method(tidy,step_measure_output_long)
+S3method(tidy,step_measure_output_wide)
 S3method(tidy,step_measure_savitzky_golay)
 export(step_measure_input_long)
 export(step_measure_input_wide)
+export(step_measure_output_long)
+export(step_measure_output_wide)
 export(step_measure_savitzky_golay)
 export(subtract_rf_baseline)
 import(recipes)
diff --git a/R/helpers.R b/R/helpers.R
index 128c3bd..9a8c979 100644
--- a/R/helpers.R
+++ b/R/helpers.R
@@ -57,4 +57,23 @@ check_for_measure <- function(x) {
                     {.fn step_measure_input_long}.")
   }
   invisible(NULL)
-}
\ No newline at end of file
+}
+
+# ------------------------------------------------------------------------------
+# Make sue that data are in the correct format.
+
+check_has_measure <- function(x, cl) {
+  step_fn <- as.character(cl[[1]])
+  step_fn <- gsub("prep\\.", "", step_fn)
+  step_fn <- paste0("`", step_fn, "()`.")
+
+
+  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)
+    rlang::abort(msg)
+  }
+}
diff --git a/man/tidy.recipe.Rd b/man/tidy.recipe.Rd
index 1c016b2..771f663 100644
--- a/man/tidy.recipe.Rd
+++ b/man/tidy.recipe.Rd
@@ -1,9 +1,11 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/input_long.R, R/input_wide.R,
-%   R/savitzky_golay.R
+% Please edit documentation in R/input_long.R, R/input_wide.R, R/output_long.R,
+%   R/output_wide.R, R/savitzky_golay.R
 \name{tidy.step_measure_input_long}
 \alias{tidy.step_measure_input_long}
 \alias{tidy.step_measure_input_wide}
+\alias{tidy.step_measure_output_long}
+\alias{tidy.step_measure_output_wide}
 \alias{tidy.step_measure_savitzky_golay}
 \title{Tidiers for measure steps}
 \usage{
@@ -11,6 +13,10 @@
 
 \method{tidy}{step_measure_input_wide}(x, ...)
 
+\method{tidy}{step_measure_output_long}(x, ...)
+
+\method{tidy}{step_measure_output_wide}(x, ...)
+
 \method{tidy}{step_measure_savitzky_golay}(x, ...)
 }
 \arguments{
diff --git a/tests/testthat/_snaps/measure_input_long.md b/tests/testthat/_snaps/measure_input_long.md
index 284193a..3e1f939 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
+    Message <cliMessage>
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -43,7 +43,7 @@
 
     Code
       print(prep_1)
-    Message
+    Message <cliMessage>
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -87,7 +87,7 @@
     Code
       recipe(water + fat + protein ~ absorp, data = na_train) %>%
         step_measure_input_long(absorp) %>% prep()
-    Condition
+    Error <recipes_error_step>
       Error in `step_measure_input_long()`:
       Caused by error in `prep()`:
       ! 'location' is required for long input data
@@ -107,7 +107,7 @@
     Code
       recipe(water + fat + protein ~ ., data = na_train) %>% step_measure_input_long(
         dplyr::everything(), location = vars(ind)) %>% prep()
-    Condition
+    Error <recipes_error_step>
       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()
-    Condition
+    Error <recipes_error_step>
       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 98d5e98..5c84336 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
+    Message <cliMessage>
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -48,7 +48,7 @@
 
     Code
       print(prep_1)
-    Message
+    Message <cliMessage>
       
       -- 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()
-    Condition
+    Error <recipes_error_step>
       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 21bb78b..639e464 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
+    Message <cliMessage>
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -45,7 +45,7 @@
 
     Code
       print(prep_1)
-    Message
+    Message <cliMessage>
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -58,7 +58,7 @@
       Training data contained 400 data points and no incomplete rows.
       
       -- Operations 
-      * Collate long analytical measurements: absorp, ind | Trained
+      * Collate long analytical measurements: absorp and ind | Trained
       * Restructure analytical measurements to long format: ~"<internal data>" |
         Trained
 
@@ -88,13 +88,3 @@
       1      1 step      measure_input_long  TRUE    FALSE potato
       2      2 step      measure_output_long TRUE    FALSE turnip
 
----
-
-    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()`.
-

From f2967c7b8e04ad426bad7d07a6b442bd6e355f1f Mon Sep 17 00:00:00 2001
From: James Wade <github@jameshwade.com>
Date: Mon, 8 Jan 2024 13:23:40 -0500
Subject: [PATCH 13/13] update snapshots

---
 tests/testthat/_snaps/measure_output_wide.md | 16 +++-------------
 1 file changed, 3 insertions(+), 13 deletions(-)

diff --git a/tests/testthat/_snaps/measure_output_wide.md b/tests/testthat/_snaps/measure_output_wide.md
index 56631da..eb6c68c 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
+    Message <cliMessage>
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -45,7 +45,7 @@
 
     Code
       print(prep_1)
-    Message
+    Message <cliMessage>
       
       -- Recipe ----------------------------------------------------------------------
       
@@ -58,7 +58,7 @@
       Training data contained 400 data points and no incomplete rows.
       
       -- Operations 
-      * Collate long analytical measurements: absorp, ind | Trained
+      * Collate long analytical measurements: absorp and ind | Trained
       * Restructure analytical measurements to wide format: ~"<internal data>" |
         Trained
 
@@ -88,13 +88,3 @@
       1      1 step      measure_input_long  TRUE    FALSE potato
       2      2 step      measure_output_wide TRUE    FALSE turnip
 
----
-
-    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()`.
-