Skip to contents

Apply Y-Axis Calibration (Response Factor)

Source: R/calibrate.R
step_measure_calibrate_y.Rd

step_measure_calibrate_y() creates a specification of a recipe step that applies a response factor or calibration function to y-axis (value) values.

Usage

step_measure_calibrate_y(
  recipe,
  response_factor = 1,
  calibration = NULL,
  measures = NULL,
  role = NA,
  trained = FALSE,
  cal_fn = NULL,
  skip = FALSE,
  id = recipes::rand_id("measure_calibrate_y")
)

Arguments

recipe

A recipe object. The step will be added to the sequence of operations for this recipe.

response_factor

A numeric value to multiply all values by. Default is 1.0 (no change). This is a simple scalar calibration.

calibration

An optional calibration function that takes value(s) and returns calibrated value(s). If provided, this takes precedence over response_factor.

measures

An optional character vector of measure column names to process. If NULL (the default), all measure columns will be processed.

role

Not used by this step since no new variables are created.

trained

A logical to indicate if the step has been trained.

cal_fn

The calibration function to apply (built during prep).

skip

A logical. Should the step be skipped when baking?

id

A character string that is unique to this step.

Value

An updated version of recipe with the new step added.

Details

Y-axis calibration is used to convert raw signal intensities to quantitative values. Common examples include:

  • Chromatography: Apply detector response factors

  • Spectroscopy: Apply molar absorptivity corrections

  • Mass spectrometry: Apply ionization efficiency corrections

Simple mode: Use response_factor to multiply all values by a constant.

Complex mode: Use calibration to provide a function for non-linear calibration curves (e.g., from fitting standards).

No selectors should be supplied to this step function. The data should be in the internal format produced by step_measure_input_wide() or step_measure_input_long().

Tidying

When you tidy() this step, a tibble with columns terms, response_factor, has_calibration, and id is returned.

See also

step_measure_calibrate_x() for x-axis calibration

Other measure-preprocessing: step_measure_absorbance(), step_measure_calibrate_x(), step_measure_derivative(), step_measure_derivative_gap(), step_measure_emsc(), step_measure_kubelka_munk(), step_measure_log(), step_measure_map(), step_measure_msc(), step_measure_normalize_istd(), step_measure_osc(), step_measure_ratio_reference(), step_measure_snv(), step_measure_subtract_blank(), step_measure_subtract_reference(), step_measure_transmittance()

Examples

library(recipes)

# Simple response factor
rec <- recipe(water + fat + protein ~ ., data = meats_long) |>
  update_role(id, new_role = "id") |>
  step_measure_input_long(transmittance, location = vars(channel)) |>
  step_measure_calibrate_y(response_factor = 2.5)

# With calibration function (e.g., log transform)
rec2 <- recipe(water + fat + protein ~ ., data = meats_long) |>
  update_role(id, new_role = "id") |>
  step_measure_input_long(transmittance, location = vars(channel)) |>
  step_measure_calibrate_y(calibration = function(x) log10(x + 0.001))