initializeFlagScheme,section-method: Establish a data-quality scheme for a section object

Description

This function stores add an item named flagScheme to the metadata slot of an object inheriting from section-class. This is a list containing two items: name and mapping, as provided in the function arguments. The purpose is both to document a flag scheme and to make it so that initializeFlags, setFlags and handleFlags can specify flags by name, as opposed to number. This is a generic function, that may be specialized to the class of object (see “Details”).

Usage

# S4 method for section
initializeFlagScheme(object, name = NULL,
  mapping = NULL, default = NULL, debug = getOption("oceDebug"))

Arguments

object

An oce object.

name

Character value naming the scheme. If this refers to a pre-defined scheme, then mapping must not be provided.

mapping

A list of named items describing the mapping from flag meaning to flag numerical value, e.g list(good=1, bad=2) might be used for a hypothetical class.

default

Integer vector of flag values that are not considered to be good. If this is not provided, but if name is "argo", "BODC", "DFO", "WHP bottle", or "WHP CTD", then a conservative value will be set automatically, equal to the list of flag values that designate bad or questionable data. For example, for name="WHP CTD", the setting will be c(1,3,4,5,6,7,9), leaving only value 2 ("acceptable" in the notation used for that flag scheme).

debug

Integer set to 0 for quiet action or to 1 for some debugging.

Value

An object with the metadata slot containing flagScheme.

Caution

This function was added in early May, 2018, and is likely to undergo changes until the autumn of that year. Use with caution.

Details

The following pre-defined schemes are available (note that the names are simplified from the phrases used in defining documentation):

name="argo" defaults mapping to list(not_assessed=0, passed_all_tests=1, probably_good=2, probably_bad=3, bad=4, averaged=7, interpolated=8, missing=9). See [1] for a deeper explanation of the meanings of these codes.
name="BODC" defaults mapping to list(no_quality_control=0, good=1, probably_good=2, probably_bad=3, bad=4, changed=5, below_detection=6, in_excess=7, interpolated=8, missing=9). See [2] for a deeper explanation of the meanings of these codes, and note that codes A and Q are not provided in oce.
name="DFO" defaults mapping to list(no_quality_control=0, appears_correct=1, appears_inconsistent=2, doubtful=3, erroneous=4, changed=5, qc_by_originator=8, missing=9). See [3] for a deeper explanation of the meanings of these codes.
name="WHP bottle" defaults mapping to list(no_information=1, no_problems_noted=2, leaking=3, did_not_trip=4, not_reported=5, discrepency=6, unknown_problem=7, did_not_trip=8, no_sample=9). See [4] for a deeper explanation of the meanings of these codes.
name="WHP CTD" defaults mapping to list(not_calibrated=1, acceptable=2, questionable=3, bad=4, not_reported=5, interpolated=6, despiked=7, missing=9). See [4] for a deeper explanation of the meanings of these codes.

References

1. The codes for "Argo" are defined at http://www.oceannetworks.ca/data-tools/data-quality

2. The codes for "BODC" are defined at http://seadatanet.maris2.nl/v_bodc_vocab_v2/browse.asp?order=conceptid&formname=search&screen=0&lib=l20

3. The codes for "DFO" are defined at http://www.dfo-mpo.gc.ca/science/data-donnees/code/list/014-eng.html

4. The codes for "WHP CTD" and "WHP bottle" are defined at https://www.nodc.noaa.gov/woce/woce_v3/wocedata_1/whp/exchange/exchange_format_desc.htm

Examples

Run this code

# NOT RUN {
data(section)
section <- read.section("a03_hy1.csv", sectionId="a03", institute="SIO",
                        ship="R/V Professor Multanovskiy", scientist="Vladimir Tereschenkov")
sectionWithFlags <- initializeFlagScheme(section, "WHP bottle")
station1 <- sectionWithFlags[["station", 1]]
str(station1[["flagScheme"]])
# }

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