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Get fluorescence and absorbance indices

Source: R/get-indices.R
get_indices.Rd

Calculates commonly used indices from absorbance and excitation–emission matrix (EEM) data. Also checks and flags index values for potential issues.

Usage

get_indices(
  eemlist,
  abslist,
  index_method = "eemanalyzeR",
  tolerance = 0.2,
  return = "wide",
  cuvle = 1,
  qaqc_dir = NA,
  arg_names = NULL
)

Arguments

eemlist

An eemlist object.

abslist

An abslist object.

index_method

Either "eemanalyzeR", "eemR", "usgs", or a custom function. See Details.

tolerance

Maximum percent deviation that the check standard can vary from the long-term values without being flagged.

return

Output format: "long" or "wide".

cuvle

Cuvette (path) length in cm.

qaqc_dir

File path to the QAQC files generated with create_mdl() and create_std(). Default is a user-specific data directory rappdirs::user_data_dir().

arg_names

Optional list of arguments passed from higher-level functions for README generation.

Value

A list with two data frames:

  • eem_index: fluorescence indices

  • abs_index: absorbance indices

Long format

If return = "long", each data frame includes:

  • sample_name: sample ID

  • meta_name: sample name in metadata (or sample_name if missing)

  • index: index name

  • value: index value

  • QAQC_flag: any associated flags

Wide format

If return = "wide", each row corresponds to a sample, and columns represent indices. Flags appear:

  • alone, if no numeric value could be returned

  • in the form VALUE_FLAG when a value exists

Details

Index methods

Three preset index sets are available:

You may also pass a custom index-generating function. See vignette("custom-indices") for instructions.

QA/QC flags

Index values are checked for common issues. Flags include:

  • DATA01: Missing data required for calculation

  • DATA02: Missing required wavelengths; value may be inaccurate

  • DATA03: Ratio denominator was zero

  • DATA04: Spectral slope could not be calculated

  • DOC01: Missing dissolved organic carbon (DOC) data

  • INF01: Infinite value

  • MDL01: All values below MDL

  • MDL02: One or more values below MDL; use cautiously

  • MDL03: Ratio index where numerator or denominator was entirely below MDL

  • NEG01: Negative value

  • STD01: Check standard value outside tolerance

  • VAL01: Value below typical range

  • VAL02: Value above typical range

Examples

indices <- get_indices(
  example_processed_eems,
  example_processed_abs,
  qaqc_dir = system.file("extdata", package = "eemanalyzeR")
)