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QA/QC flags for missing data

Source: R/flag-missing.R
flag_missing.Rd

Checks if a metric can't be calculated or may be inaccurate due to missing wavelengths required to calculate that metric.

Usage

flag_missing(x, ex = NULL, em = NULL, wl = NULL, all = TRUE)

Arguments

x

An eemlist, eem, abslist, or abs object.

ex

A vector of excitation wavelengths required to calculate the index. Only needed if x is an eemlist or eem.

em

A vector of emission wavelengths required to calculate the index. Only needed if x is an eemlist or eem.

wl

A vector of wavelengths required to calculate the index. Only needed if x is an abslist or abs.

all

If TRUE index will not be calculated if some wavelengths are missing, returning "DATA01".

Value

A vector containing text flags and NA values. Possible values:

  • "DATA_01": Missing data required to calculate the index.

  • "DATA_02": Missing some wavelengths required to calculate the index; value may be inaccurate.

  • NA: No missing data; no flag needed.

Examples

# checking absorbance data
# data exists
flag_missing(example_abs, wl = 400)
#> [1] NA NA NA NA

# data doesn't exist
flag_missing(example_abs, wl = 100)
#> [1] "DATA01" "DATA01" "DATA01" "DATA01"

# some data exists, still calculate
flag_missing(example_abs, wl = 100:254, all = FALSE)
#> [1] "DATA02" "DATA02" "DATA02" "DATA02"

# checking fluorescence data
# data exists
flag_missing(example_eems, ex = 270:280, em = 300:320)
#> [1] NA NA NA NA NA NA NA NA

# data doesn't exist
flag_missing(example_eems, ex = 100:150, em = 300:320)
#> [1] "DATA01" "DATA01" "DATA01" "DATA01" "DATA01" "DATA01" "DATA01" "DATA01"

# some data exists, still calculate
flag_missing(example_eems, ex = 100:350, em = 300:320, all = FALSE)
#> [1] "DATA02" "DATA02" "DATA02" "DATA02" "DATA02" "DATA02" "DATA02" "DATA02"