This function adds an item named flagScheme
to the metadata slot of an object inheriting from
ctd. 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,
default = NULL,
update = NULL,
debug = 0
)An object with the metadata slot containing flagScheme.
An oce object.
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.
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.
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.
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.
an integer set to 0 for quiet action or to 1 for some debugging.
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.
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
Other functions relating to data-quality flags:
defaultFlags(),
handleFlags,adp-method,
handleFlags,argo-method,
handleFlags,ctd-method,
handleFlags,oce-method,
handleFlags,section-method,
handleFlags(),
initializeFlagScheme,oce-method,
initializeFlagScheme,section-method,
initializeFlagSchemeInternal(),
initializeFlagScheme(),
initializeFlags,adp-method,
initializeFlags,oce-method,
initializeFlagsInternal(),
initializeFlags(),
setFlags,adp-method,
setFlags,ctd-method,
setFlags,oce-method,
setFlags()
Other things related to ctd data:
CTD_BCD2014666_008_1_DN.ODF.gz,
[[,ctd-method,
[[<-,ctd-method,
as.ctd(),
cnvName2oceName(),
ctd-class,
ctd.cnv.gz,
ctdDecimate(),
ctdFindProfilesRBR(),
ctdFindProfiles(),
ctdRaw,
ctdRepair(),
ctdTrim(),
ctd_aml.csv.gz,
ctd,
d200321-001.ctd.gz,
d201211_0011.cnv.gz,
handleFlags,ctd-method,
initialize,ctd-method,
oceNames2whpNames(),
oceUnits2whpUnits(),
plot,ctd-method,
plotProfile(),
plotScan(),
plotTS(),
read.ctd.aml(),
read.ctd.itp(),
read.ctd.odf(),
read.ctd.odv(),
read.ctd.sbe(),
read.ctd.ssda(),
read.ctd.woce.other(),
read.ctd.woce(),
read.ctd(),
setFlags,ctd-method,
subset,ctd-method,
summary,ctd-method,
woceNames2oceNames(),
woceUnit2oceUnit(),
write.ctd()