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. 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,
  update = NULL,
  debug = getOption("oceDebug")
)

Arguments

object

An oce object.

name

a character value naming the scheme. If this refers to a pre-defined scheme, then mapping must not be provided, because doing so would contradict the pre-defined scheme, defeating its purpose of providing concreteness and clarity.

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

an 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, which corresponds with "acceptable" in the notation used for that flag scheme.

update

a logical value indicating whether the scheme provided is to update an existing scheme. The default value, FALSE, prevents such an attempt to alter an existing flag scheme, if one is already embedded in object.

debug

an integer set to 0 for quiet action or to 1 for some debugging.

Value

An object with the metadata slot containing flagScheme.

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 OLD (prior to June 10, 2020)

list(not_assessed=0, passed_all_tests=1, probably_good=2,
     probably_bad=3, bad=4, averaged=7,
     interpolated=8, missing=9)

NEW (after June 10, 2020)

list(not_assessed=0, passed_all_tests=1, probably_good=2,
     probably_bad=3, bad=4, changed=5, not_used_6=6, not_used_7=7,
     estimated=8, missing=9)

See reference 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 reference 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 reference 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 reference 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 reference 4 for a deeper explanation of the meanings of these codes.

References

The codes for "argo" are derived from information in Table 4.1 of Wong, Annie, Robert Keeley, Thierry Carval, and Argo Data Management Team (8 January 2020), "Argo Quality Control Manual for CTD and Trajectory Data, Version 3.3," available at https://archimer.ifremer.fr/doc/00228/33951/ as of June 2020.
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
The codes for "DFO" are defined at http://www.dfo-mpo.gc.ca/science/data-donnees/code/list/014-eng.html
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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