initializeFlagScheme,ctd-method {oce} | R Documentation |
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 signature 'ctd' initializeFlagScheme(object, name = NULL, mapping = NULL, debug = getOption("oceDebug"))
object |
An oce object. |
name |
Character value naming the scheme. If this refers
to a pre-defined scheme, then |
mapping |
A list of named items describing the mapping from
flag meaning to flag numerical value, e.g |
debug |
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
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.
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.
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