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Calculate method detection limits (MDL)

Source: R/create-mdl.R
create_mdl.Rd

The method detection limit (MDL) is the minimum signal at which we can confidently distinguish a measurement from zero and from analytical blanks. Here, the MDL is calculated using the approach proposed by Hansen et al. (2018): MDL = mean(long-term blank) + 3 × SD(long-term blank).

Usage

create_mdl(
  dir,
  meta_name = NULL,
  sheet = NULL,
  iblank = "BEM",
  type = "eem",
  recursive = FALSE,
  qaqc_dir = NULL
)

Source

Hansen, A. M., Fleck, J., Kraus, T. E. C., Downing, B. D., von Dessonneck, T., & Bergamaschi, B. (2018). Procedures for using the Horiba Scientific Aqualog® fluorometer to measure absorbance and fluorescence from dissolved organic matter (USGS Numbered Series No. 2018-1096). U.S. Geological Survey. doi:10.3133/ofr20181096

Arguments

dir

Path to a folder containing long-term EEMs and/or absorbance files. All files in this directory will be loaded.

meta_name

Name of the metadata file. Optional if the metadata file is the only .xlsx or .csv file in dir. If not specified, the function attempts to find a single metadata file and errors if multiple files are present.

sheet

Name of the sheet containing metadata (only required if the metadata is not on the first sheet of an .xlsx file).

iblank

Optional. A character string containing a base::regular expression used to identify instrument blanks.

type

Which MDL to calculate: either "eem" or "abs".

recursive

Logical. Should the function recursively search directories?

qaqc_dir

Directory in which to save the QAQC .rds file. Default: a user-specific data directory via rappdirs::user_data_dir(). If FALSE, the function returns the MDL object instead of saving it.

Value

  • If qaqc_dir = FALSE: returns an eem or abs object containing MDL values.

  • Otherwise: saves an .rds file containing the MDL object and invisibly returns the file path.

Details

To calculate the MDL, you need:

  • A directory containing analytical blanks and instrument blanks (fewer than 20 blanks triggers a warning). Note: sample names must be unique.

  • A metadata file for the blanks containing, at minimum, integration time and Raman area, formatted as a metadata file described in metadata.

Examples

eem_mdl <- create_mdl(
  file.path(system.file("extdata", package = "eemanalyzeR"), "long-term-blanks"),
  type = "eem",
  qaqc_dir = FALSE
)
#> No Meta file specified, using:
#> /home/runner/work/_temp/Library/eemanalyzeR/extdata/long-term-blanks/longtermblank-metadata.csv
#> NOTE: removed previous 'readme' file
#> Warning: Unable to import file: /home/runner/work/_temp/Library/eemanalyzeR/extdata/long-term-blanks/longtermblank1ABS.dat.
#> Please use the 'pattern' and 'skip' arguments to ensure only EEM's files are selected.
#> Warning: Unable to import file: /home/runner/work/_temp/Library/eemanalyzeR/extdata/long-term-blanks/longtermblank2ABS.dat.
#> Please use the 'pattern' and 'skip' arguments to ensure only EEM's files are selected.
#> Warning: Unable to import file: /home/runner/work/_temp/Library/eemanalyzeR/extdata/long-term-blanks/longtermblank3ABS.dat.
#> Please use the 'pattern' and 'skip' arguments to ensure only EEM's files are selected.
#> Warning: Unable to import file: /home/runner/work/_temp/Library/eemanalyzeR/extdata/long-term-blanks/longtermblank4ABS.dat.
#> Please use the 'pattern' and 'skip' arguments to ensure only EEM's files are selected.
#> Warning: Unable to import file: /home/runner/work/_temp/Library/eemanalyzeR/extdata/long-term-blanks/longtermblank5ABS.dat.
#> Please use the 'pattern' and 'skip' arguments to ensure only EEM's files are selected.
#> Warning: Unable to import file: /home/runner/work/_temp/Library/eemanalyzeR/extdata/long-term-blanks/longtermblank6ABS.dat.
#> Please use the 'pattern' and 'skip' arguments to ensure only EEM's files are selected.
#> Warning: Calculating MDL based on less than 20 samples, MDL may be unreliable

plot(eem_mdl)