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Conventional Calibration for SEC Using Narrow Standards

Source: R/step_sec_conventional_cal.R
step_sec_conventional_cal.Rd

step_sec_conventional_cal() creates a specification of a recipe step that fits a calibration curve from narrow molecular weight standards and applies it to convert elution time/volume to molecular weight.

Usage

step_sec_conventional_cal(
  recipe,
  measures = NULL,
  standards = NULL,
  calibration = NULL,
  fit_type = c("cubic", "quadratic", "linear", "fifth", "gam"),
  extrapolation = c("warn", "none", "linear"),
  output_col = "mw",
  log_output = TRUE,
  role = NA,
  trained = FALSE,
  skip = FALSE,
  id = recipes::rand_id("sec_conventional_cal")
)

Arguments

recipe

A recipe object.

measures

Character vector of measure columns to apply calibration to. If NULL, uses all measure columns.

standards

A data frame containing calibration standards with columns:

  • location (or time, volume, retention): Elution position

  • log_mw (or mw): Molecular weight (will be log-transformed if mw) Required unless calibration is provided.

calibration

A pre-loaded calibration object from load_sec_calibration(). When provided, skips fitting and uses the saved calibration directly. Takes precedence over standards.

fit_type

Type of fit for the calibration curve:

  • "cubic" (default): Third-order polynomial

  • "quadratic": Second-order polynomial

  • "linear": First-order (linear) fit

  • "fifth": Fifth-order polynomial

  • "gam": Generalized Additive Model with cubic splines (requires mgcv)

extrapolation

How to handle data outside the calibration range:

  • "warn" (default): Extrapolate but warn

  • "none": Return NA for out-of-range values

  • "linear": Use linear extrapolation at boundaries

output_col

Name for the output molecular weight column. Default is "mw".

log_output

Logical. If TRUE (default), output column contains log10(MW). If FALSE, output contains MW in Daltons.

role

Role for generated columns.

trained

Logical indicating if the step has been trained.

skip

Logical. Should the step be skipped when baking?

id

Unique step identifier.

Value

An updated recipe with the new step added.

Details

This step performs conventional (also called relative) SEC calibration using narrow dispersity standards of known molecular weight. The calibration curve relates elution position to log(MW):

$$\log_{10}(M) = f(V_e)$$

where f is a polynomial function and V_e is the elution volume or time.

Calibration Curve Fitting:

The calibration is fit using orthogonal polynomials for numerical stability. At least 3 standards are required for cubic fits, 4 for quadratic, etc.

Important Considerations:

  • Standards should bracket the MW range of interest

  • Calibration is polymer-specific (different polymers have different hydrodynamic volumes at the same MW)

  • For cross-polymer comparisons, use universal calibration instead (step_sec_universal_cal)

Fit Quality Metrics: The tidy() method returns calibration coefficients and R-squared values for assessing fit quality. R² > 0.999 is typical for good calibrations.

See also

Other sec-calibration: load_sec_calibration(), save_sec_calibration(), sec_calibration_standards, sec_pmma_standards, sec_ps_standards, step_sec_broad_standard(), step_sec_universal_cal()

Examples

if (FALSE) { # \dontrun{
library(recipes)
library(measure)

# Create calibration standards data
ps_standards <- data.frame(
  retention = c(12.5, 13.2, 14.1, 15.0, 16.2, 17.5),
  log_mw = c(6.0, 5.5, 5.0, 4.5, 4.0, 3.5)
)

# Apply conventional calibration
rec <- recipe(~., data = polymer_data) |>
  step_measure_input_long(ri, location = vars(time), col_name = "ri") |>
  step_sec_baseline() |>
  step_sec_conventional_cal(
    standards = ps_standards,
    fit_type = "cubic"
  ) |>
  prep()

# Check calibration quality
tidy(rec, number = 3)
} # }