Apply X-Axis Calibration

step_measure_calibrate_x() creates a specification of a recipe step that transforms the x-axis (location) values using a calibration function or calibration data.

Usage

step_measure_calibrate_x(
  recipe,
  calibration,
  from = "x",
  to = "y",
  method = "spline",
  extrapolate = FALSE,
  measures = NULL,
  role = NA,
  trained = FALSE,
  cal_fn = NULL,
  skip = FALSE,
  id = recipes::rand_id("measure_calibrate_x")
)

Arguments

recipe

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

calibration

The calibration to apply. Can be:

• A data.frame with columns specified by from and to

• A function that takes location values and returns calibrated values

from

Column name in calibration data.frame containing original x values. Default is "x".

to

Column name in calibration data.frame containing calibrated values. Default is "y".

method

Interpolation method when using calibration data.frame:

• "linear": Linear interpolation

• "spline" (default): Cubic spline interpolation

extrapolate

Logical. If TRUE, allow extrapolation outside the calibration range. If FALSE (default), values outside the range will return NA for linear interpolation or use spline extrapolation.

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 created during training.

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

X-axis calibration is commonly used to convert raw measurement units to physically meaningful values. Common examples include:

• GPC/SEC: Convert retention time to molecular weight (via log MW)

• Mass spectrometry: Apply m/z calibration corrections

• Spectroscopy: Convert pixel or channel numbers to wavelength/wavenumber

The calibration can be provided as either:

1. Calibration data: A data.frame with known x→y mappings. The step will build an interpolation function during prep().

2. Calibration function: A function that directly transforms x values.

Warning: This step modifies the location column. Subsequent steps will see the calibrated values. Make sure your calibration is appropriate for your data range.

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, method, extrapolate, and id is returned.

See also

step_measure_calibrate_y() for y-axis calibration

Other measure-preprocessing: step_measure_absorbance(), step_measure_calibrate_y(), 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)

# Example: GPC molecular weight calibration
# Calibration standards: retention_time -> log(MW)
gpc_cal <- data.frame(
  retention_time = c(10, 12, 14, 16, 18),
  log_mw = c(6.5, 5.8, 5.0, 4.2, 3.5)
)

# Note: meats_long doesn't have retention time, this is illustrative
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_x(
    calibration = function(x) log10(x + 1),  # Example transformation
    method = "spline"
  )

# With calibration data
# rec <- recipe(...) |>
#   step_measure_calibrate_x(
#     calibration = gpc_cal,
#     from = "retention_time",
#     to = "log_mw",
#     method = "spline"
#   )