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USGS methods for fluorescence and absorbance indices

Source: R/usgs-indices.R
usgs_indices.Rd

Calculates commonly used absorbance and fluorescence optical indices from eemlist and abslist. These indices are those commonly used by the U.S. Geological Survey. For detailed descriptions and references, see Hansen et al. 2018 (Tables 1 and 8).

Usage

usgs_indices(eemlist, abslist, cuvle = 1, qaqc_dir = NA)

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

eemlist

An eemlist object.

abslist

An abslist object.

cuvle

Cuvette (path) length in cm.

qaqc_dir

File path to the QAQC files generated with create_mdl() and create_std(). Default is NA, which results in NO QAQC CHECKS.

Value

A list with two elements:

  • eem_index: a data.frame of all fluorescence indices. Each row corresponds to a single index for a sample.

  • abs_index: a data.frame of all absorbance indices. Each row corresponds to a single index for a sample.

Each data.frame contains the following columns:

  • sample_id: sample identifier for the sample (if provided, otherwise uses sample: the sample's file name)

  • sample_name: sample name or description (if provided, otherwise uses sample: the sample's file name)

  • index: name of the index

  • value: calculated value of the index

Note

  • If absorbance is not at a 1 nm interval, it will be interpolated using zoo::na.approx(), which fills in missing values using linear interpolation.

  • If EEM data is not at a 1 nm interval, fluorescence will be interpolated using pracma::interp2().

Examples

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