ir (version 0.4.1)

ir_variance_region: Computes the variance of a spectrum in an ir object in a given region

Description

ir_variance_region takes a spectrum x and, depending on the arguments computes the following summary:

if subtract_smoothed = FALSE

it computes the variance of the intensity values for each spectrum in x. If in addition range is not NULL, it computes the variance only for the region(s) represented by range.

if subtract_smoothed = TRUE

it smoothes x, subtracts the smoothed x from the unsmoothed x and computes the variance of the difference intensity values. If in addition range is not NULL, it computes the variance only for the region(s) represented by range.

Usage

ir_variance_region(
  x,
  subtract_smoothed = FALSE,
  do_normalize = FALSE,
  normalize_method,
  ...,
  range = NULL
)

Value

x with two additional columns:

variance

A numeric vector with the computed variances of the intensity values for the respective spectra.

n_variance

An integer vector with the number of intensity values used during computing the variance.

Arguments

x

An object of class ir. These are the spectra for which to compute the variance.

subtract_smoothed

A logical value. If subtract_smoothed = TRUE, x is copied, the copy smoothed using ir_smooth with method = "sg" and subtracted from x before the variance of the intensity values from x is computed. This allows e.g. to estimate the noise level in a specific region of spectra. If subtract_smoothed = FALSE (the default), nothing is subtracted from x before computing the variance of the intensity values.

do_normalize

A logical value. If set to TRUE, the spectra in x are normalized after subtraction of a smoothed version, else no normalization is performed.

normalize_method

See ir_normalize().

...

Arguments passed to ir_smooth() (except for method which is always set to "sg" if subtract_smoothed is TRUE). If subtract_smoothed = FALSE, these arguments will be ignored.

range

See ir_clip(). This is the range for which the variance of the intensity values will be computed.

Examples

# Whole spectra variance
x1 <-
   ir::ir_sample_data |>
   ir::ir_variance_region(
      subtract_smoothed = FALSE,
      do_normalize = TRUE,
      normalize_method = "area",
      range = NULL
   )

# Spectra variance, but only from a specific region
range <- data.frame(start = 2700, end = 2800)

x2 <-
   ir::ir_sample_data |>
   ir::ir_normalize(method = "area") |>
   ir::ir_variance_region(
      subtract_smoothed = FALSE,
      do_normalize = TRUE,
      normalize_method = "area",
      range = range
   )

# Spectra variance after subtracting a smoothed version of the spectra and
# only from a specific region
x3 <-
   ir::ir_sample_data %>%
   ir::ir_variance_region(
      subtract_smoothed = TRUE,
      do_normalize = FALSE,
      range = range,
      p = 3, n = 31, ts = 1, m = 0
   )