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Get fluorescence within a specified range

Source: R/get-fluorescence.R
get_fluorescence.Rd

Gets fluorescence within a range of excitation and emission wavelengths and returns either the maximum value or the sum across that range. Missing values are interpolated using pracma::interp2().

Usage

get_fluorescence(eem, ex, em, stat = "max", norm = FALSE)

Arguments

eem

An eem or eemlist object.

ex

A vector of excitation wavelengths.

em

A vector of emission wavelengths.

stat

A string specifying the statistic to return:

  • "max": return the maximum value (default)

  • "sum": return the sum of values

norm

Logical. If TRUE, divides the index value by the DOC concentration. Metadata must be added using add_metadata(), otherwise NA will be returned.

Value

A numeric vector of fluorescence values. Returns NA if values cannot be extracted.

Examples

pA <- get_fluorescence(example_eems, ex = 250:260, em = 380:480)
pD <- get_fluorescence(example_eems, ex = 390, em = 509)

pA_sum <- get_fluorescence(
  example_eems,
  ex = 250:260,
  em = 380:480,
  stat = "sum"
)

eemlist <- add_metadata(metadata, example_eems)

pA_docnorm <- get_fluorescence(
  eemlist,
  ex = 250:260,
  em = 380:480,
  norm = TRUE
)