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Default package methods for fluorescence and absorbance indices

Source: R/eemanalyzeR-indices.R
eemanalyzeR_indices.Rd

Calculates commonly used absorbance and fluorescence optical indices from eemlist and abslist. For detailed descriptions and references for indices, see the vignette vignette("eemanalyzeR-indices").

Usage

eemanalyzeR_indices(eemlist, abslist, cuvle = 1, qaqc_dir = NULL)

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 a user-specific data directory rappdirs::user_data_dir().

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_name: name of the sample from the EEM or absorbance list

  • meta_name: sample name from metadata if provided; otherwise same as sample_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 <- eemanalyzeR_indices(
  example_processed_eems,
  example_processed_abs,
  qaqc_dir = system.file("extdata", package = "eemanalyzeR")
)