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Check whether an EEM or absorbance sample is above the MDL

Source: R/check-mdl.R
check_mdl.Rd

Checks whether values in an eem or abs object are above the method detection limit (MDL) for a specified set of wavelengths or excitation–emission pairs.

Usage

check_eem_mdl(eem, mdl = NULL, ex, em, vals = FALSE)

check_abs_mdl(abs, mdl = NULL, wl, vals = FALSE)

Arguments

eem

An eem or eemlist object.

mdl

An eem or abs object containing MDL data. If no MDL is provided, NA is returned.

ex

A vector of excitation wavelengths.

em

A vector of emission wavelengths.

vals

If TRUE, returns actual values, otherwise returns just flags.

abs

An abs or abslist object.

wl

A vector of absorbance wavelengths.

Value

If vals = FALSE, returns one of:

  • "MDL01": all values are below the MDL

  • "MDL02": some values are below the MDL

  • NA: all values are above the MDL

If vals = TRUE, returns:

  • A data.frame containing wavelengths, observed values, and MDL values

Examples

# Load MDL data
eem_mdl <- readRDS(file.path(
  system.file("extdata", package = "eemanalyzeR"),
  "eem-mdl.rds"
))

abs_mdl <- readRDS(file.path(
  system.file("extdata", package = "eemanalyzeR"),
  "abs-mdl.rds"
))

# Single EEM sample
check_eem_mdl(example_processed_eems[[1]], eem_mdl,
              ex = 270:280, em = 300:320)
#> [1] "MDL01"

# EEM list
check_eem_mdl(example_processed_eems, eem_mdl,
              ex = 270:280, em = 300:320)
#> [1] "MDL01" NA      NA      NA     

# Single absorbance sample
check_abs_mdl(example_processed_abs[[2]], abs_mdl, wl = 254)
#> [1] NA

# Absorbance list
check_abs_mdl(example_processed_abs, abs_mdl, wl = 254)
#> [1] "MDL01" NA      NA      NA