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Format index and flag data

Source: R/format-index.R
format_index.Rd

Combines index values, QA/QC flags, and sample metadata into a clean data.frame for further processing. Any values flagged as "MDL01" (below detection limit) are removed and not reported.

Usage

format_index(x, index, value, flag)

Arguments

x

An eemlist or abslist object.

index

A character string giving the name of the index.

value

Index values. Use get_fluorescence() or get_absorbance() to generate these values.

flag

Flag values, the same length as value.

Value

A data frame with four columns:

  • sample_name: the sample name

  • meta_name: the sample name in metadata (if provided), otherwise repeats sample_name

  • index: the name of the index

  • value: the index value (with MDL01 values removed)

Examples

ex <- 240:260
em <- 300:320

vals <- get_fluorescence(example_eems, ex, em, stat = "max")
flags <- flag_missing(example_eems, ex = ex, em = em, all = FALSE)

index_formatted <- format_index(
  x = example_eems,
  index = "test_index",
  value = vals,
  flag = flags
)