This function stores add an item named flagScheme
to the metadata slot of an object inheriting from
ctd-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”).
# S4 method for ctd
initializeFlagScheme(object, name = NULL,
mapping = NULL, debug = getOption("oceDebug"))An oce object.
Character value naming the scheme. If this refers
to a pre-defined scheme, then mapping must not be provided.
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.
Integer set to 0 for quiet action or to 1 for some debugging.
An object with the metadata slot containing flagScheme.
This function was added in early May, 2018, and is likely to undergo changes until the autumn of that year. Use with caution.
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.
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
Other functions relating to data-quality flags: defaultFlags,
handleFlags,adp-method,
handleFlags,argo-method,
handleFlags,ctd-method,
handleFlags,section-method,
handleFlags,
initializeFlagScheme,oce-method,
initializeFlagScheme,section-method,
initializeFlagScheme,
initializeFlags,adp-method,
initializeFlags,oce-method,
initializeFlags,
setFlags,adp-method,
setFlags,ctd-method,
setFlags,oce-method, setFlags
Other things related to ctd data: [[,ctd-method,
[[<-,ctd-method, as.ctd,
cnvName2oceName, ctd-class,
ctdDecimate, ctdFindProfiles,
ctdRaw, ctdTrim,
ctd, handleFlags,ctd-method,
initialize,ctd-method,
oceNames2whpNames,
oceUnits2whpUnits,
plot,ctd-method, plotProfile,
plotScan, plotTS,
read.ctd.itp, read.ctd.odf,
read.ctd.sbe,
read.ctd.woce.other,
read.ctd.woce, read.ctd,
setFlags,ctd-method,
subset,ctd-method,
summary,ctd-method,
woceNames2oceNames,
woceUnit2oceUnit, write.ctd