From 809da4a39814d923c48a004fb5c843670fe66974 Mon Sep 17 00:00:00 2001
From: simonpcouch <simonpatrickcouch@gmail.com>
Date: Mon, 22 Apr 2024 15:04:35 -0500
Subject: [PATCH] simplify file structure

renames files that define an `adjust_*()` function and associated method as `adjust_function_name.R`. helps to differentiate this relatively homogenous file type from other kinds of source files.
---
 ...uivocal-zone.R => adjust-equivocal-zone.R} |  0
 ...bration.R => adjust-numeric-calibration.R} |  0
 R/{numeric-range.R => adjust-numeric-range.R} |  0
 ...s-custom.R => adjust-predictions-custom.R} |  0
 ...ion.R => adjust-probability-calibration.R} |  0
 ...shold.R => adjust-probability-threshold.R} |  0
 R/container.R                                 |  2 +-
 R/operation.R                                 | 29 ------------------
 R/utils.R                                     | 30 +++++++++++++++++++
 R/validation-rules.R                          | 12 ++++----
 man/adjust_equivocal_zone.Rd                  |  2 +-
 man/adjust_numeric_calibration.Rd             |  2 +-
 man/adjust_numeric_range.Rd                   |  2 +-
 man/adjust_predictions_custom.Rd              |  2 +-
 man/adjust_probability_calibration.Rd         |  2 +-
 man/adjust_probability_threshold.Rd           |  2 +-
 16 files changed, 43 insertions(+), 42 deletions(-)
 rename R/{equivocal-zone.R => adjust-equivocal-zone.R} (100%)
 rename R/{numeric-calibration.R => adjust-numeric-calibration.R} (100%)
 rename R/{numeric-range.R => adjust-numeric-range.R} (100%)
 rename R/{predictions-custom.R => adjust-predictions-custom.R} (100%)
 rename R/{probability-calibration.R => adjust-probability-calibration.R} (100%)
 rename R/{prob-threshold.R => adjust-probability-threshold.R} (100%)
 delete mode 100644 R/operation.R

diff --git a/R/equivocal-zone.R b/R/adjust-equivocal-zone.R
similarity index 100%
rename from R/equivocal-zone.R
rename to R/adjust-equivocal-zone.R
diff --git a/R/numeric-calibration.R b/R/adjust-numeric-calibration.R
similarity index 100%
rename from R/numeric-calibration.R
rename to R/adjust-numeric-calibration.R
diff --git a/R/numeric-range.R b/R/adjust-numeric-range.R
similarity index 100%
rename from R/numeric-range.R
rename to R/adjust-numeric-range.R
diff --git a/R/predictions-custom.R b/R/adjust-predictions-custom.R
similarity index 100%
rename from R/predictions-custom.R
rename to R/adjust-predictions-custom.R
diff --git a/R/probability-calibration.R b/R/adjust-probability-calibration.R
similarity index 100%
rename from R/probability-calibration.R
rename to R/adjust-probability-calibration.R
diff --git a/R/prob-threshold.R b/R/adjust-probability-threshold.R
similarity index 100%
rename from R/prob-threshold.R
rename to R/adjust-probability-threshold.R
diff --git a/R/container.R b/R/container.R
index 627c877..0b770d2 100644
--- a/R/container.R
+++ b/R/container.R
@@ -57,7 +57,7 @@ new_container <- function(mode, type, operations, columns, ptype, call) {
   }
 
   # validate operation order and check duplicates
-  validate_oper_order(operations, mode, call)
+  validate_order(operations, mode, call)
 
   # check columns
   res <- list(
diff --git a/R/operation.R b/R/operation.R
deleted file mode 100644
index dee6d76..0000000
--- a/R/operation.R
+++ /dev/null
@@ -1,29 +0,0 @@
-# These values are used to specify "what will we need for the adjustment?" and
-# "what will we change?". For the outputs, we cannot change the probabilities
-# without changing the classes. This is important because we are going to have
-# to define constrains on the order of adjustments.
-
-input_vals <- c("numeric", "probability", "class", "everything")
-output_vals <- c("numeric", "probability_class", "class", "everything")
-
-new_operation <- function(cls, inputs, outputs, arguments, results = list(trained = FALSE), ...) {
-  inputs <- arg_match0(inputs, input_vals)
-  outputs <- arg_match0(outputs, output_vals)
-
-  if (!any(names(results) == "trained")) {
-    cli_abort("The {.arg results} slot requires a logical variable called \\
-                   {.val trained}")
-  } else {
-    check_logical(results$trained)
-  }
-
-  res <-
-    list(
-      inputs = inputs,
-      outputs = outputs,
-      arguments = arguments,
-      results = results
-    )
-  class(res) <- c(cls, "operation")
-  res
-}
diff --git a/R/utils.R b/R/utils.R
index 3f34f2b..bcd1464 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -15,3 +15,33 @@ no_param <-
     component = character(0),
     component_id = character(0)
   )
+
+# These values are used to specify "what will we need for the adjustment?" and
+# "what will we change?". For the outputs, we cannot change the probabilities
+# without changing the classes. This is important because we are going to have
+# to define constrains on the order of adjustments.
+
+input_vals <- c("numeric", "probability", "class", "everything")
+output_vals <- c("numeric", "probability_class", "class", "everything")
+
+new_operation <- function(cls, inputs, outputs, arguments, results = list(trained = FALSE), ...) {
+  inputs <- arg_match0(inputs, input_vals)
+  outputs <- arg_match0(outputs, output_vals)
+
+  if (!any(names(results) == "trained")) {
+    cli_abort("The {.arg results} slot requires a logical variable called \\
+                   {.val trained}")
+  } else {
+    check_logical(results$trained)
+  }
+
+  res <-
+    list(
+      inputs = inputs,
+      outputs = outputs,
+      arguments = arguments,
+      results = results
+    )
+  class(res) <- c(cls, "operation")
+  res
+}
diff --git a/R/validation-rules.R b/R/validation-rules.R
index 4402c63..a6a74a7 100644
--- a/R/validation-rules.R
+++ b/R/validation-rules.R
@@ -1,5 +1,5 @@
-validate_oper_order <- function(ops, mode, call) {
-  oper_data <-
+validate_order <- function(ops, mode, call) {
+  orderings <-
     tibble::new_tibble(list(
       name = purrr::map_chr(ops, ~ class(.x)[1]),
       input = purrr::map_chr(ops, ~ .x$inputs),
@@ -10,16 +10,16 @@ validate_oper_order <- function(ops, mode, call) {
     ))
 
   if (length(ops) < 2) {
-    return(invisible(oper_data))
+    return(invisible(orderings))
   }
 
   if (mode == "classification") {
-    check_classification_order(oper_data, call)
+    check_classification_order(orderings, call)
   } else {
-    check_regression_order(oper_data, call)
+    check_regression_order(orderings, call)
   }
 
-  invisible(oper_data)
+  invisible(orderings)
 }
 
 check_classification_order <- function(x, call) {
diff --git a/man/adjust_equivocal_zone.Rd b/man/adjust_equivocal_zone.Rd
index 3967dbc..705f41e 100644
--- a/man/adjust_equivocal_zone.Rd
+++ b/man/adjust_equivocal_zone.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/equivocal-zone.R
+% Please edit documentation in R/adjust-equivocal-zone.R
 \name{adjust_equivocal_zone}
 \alias{adjust_equivocal_zone}
 \title{Apply an equivocal zone to a binary classification model.}
diff --git a/man/adjust_numeric_calibration.Rd b/man/adjust_numeric_calibration.Rd
index 2244960..6c13706 100644
--- a/man/adjust_numeric_calibration.Rd
+++ b/man/adjust_numeric_calibration.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/numeric-calibration.R
+% Please edit documentation in R/adjust-numeric-calibration.R
 \name{adjust_numeric_calibration}
 \alias{adjust_numeric_calibration}
 \title{Re-calibrate numeric predictions}
diff --git a/man/adjust_numeric_range.Rd b/man/adjust_numeric_range.Rd
index a611687..08911f8 100644
--- a/man/adjust_numeric_range.Rd
+++ b/man/adjust_numeric_range.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/numeric-range.R
+% Please edit documentation in R/adjust-numeric-range.R
 \name{adjust_numeric_range}
 \alias{adjust_numeric_range}
 \title{Truncate the range of numeric predictions}
diff --git a/man/adjust_predictions_custom.Rd b/man/adjust_predictions_custom.Rd
index 1a1e417..4f54ced 100644
--- a/man/adjust_predictions_custom.Rd
+++ b/man/adjust_predictions_custom.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/predictions-custom.R
+% Please edit documentation in R/adjust-predictions-custom.R
 \name{adjust_predictions_custom}
 \alias{adjust_predictions_custom}
 \title{Change or add variables}
diff --git a/man/adjust_probability_calibration.Rd b/man/adjust_probability_calibration.Rd
index d71f1c0..65e0392 100644
--- a/man/adjust_probability_calibration.Rd
+++ b/man/adjust_probability_calibration.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/probability-calibration.R
+% Please edit documentation in R/adjust-probability-calibration.R
 \name{adjust_probability_calibration}
 \alias{adjust_probability_calibration}
 \title{Re-calibrate classification probability predictions}
diff --git a/man/adjust_probability_threshold.Rd b/man/adjust_probability_threshold.Rd
index 30e2af6..ea227dd 100644
--- a/man/adjust_probability_threshold.Rd
+++ b/man/adjust_probability_threshold.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/prob-threshold.R
+% Please edit documentation in R/adjust-probability-threshold.R
 \name{adjust_probability_threshold}
 \alias{adjust_probability_threshold}
 \title{Change the event threshold}