Data-quality flags are stored in the metadata
slot of '>oce objects in a
list named flags.
The present function (a generic that has specialized versions
for various data classes) provides a way to
manipulate the contents of the data slot, based on
such data-quality flags. For example, a common operation is to replace
erroneous data with NA.
If the flags within object's metadata slot is empty,
then object is returned, unaltered.
Otherwise, handleFlags examines object@metadata$flags
in the context of the flags argument, and then
carries out actions that are specified by the actions argument.
By default, this sets the returned data entries to NA,
wherever the corresponding metadata$flag values
signal unreliable data. To maintain a hint as to why
data were changed, metadata$flags in the
returned value is a direct copy of the corresponding
entry in object.
# S4 method for argo
handleFlags(
object,
flags = NULL,
actions = NULL,
where = NULL,
debug = getOption("oceDebug")
)A list specifying flag values upon which actions will be taken. This can take two forms.
In the first form, the
list has named elements each containing a vector of integers. For example,
salinities flagged with values of 1 or 3:9 would be specified
by flags=list(salinity=c(1,3:9)). Several data items can be specified,
e.g. flags=list(salinity=c(1,3:9), temperature=c(1,3:9)) indicates
that the actions are to take place for both salinity and temperature.
In the second form, flags is a list holding a single unnamed vector, and
this means to apply the actions to all the data entries. For example,
flags=list(c(1,3:9)) means to apply not just to salinity and temperature,
but to everything within the data slot.
If flags is not provided, then defaultFlags() is called, to try to
determine a reasonable default.
an optional list that contains items with
names that match those in the flags argument. If actions
is not supplied, the default will be to set all values identified by
flags to NA; this can also be specified by
specifying actions=list("NA"). It is also possible to specify
functions that calculate replacement values. These are provided
with object as the single argument, and must return a
replacement for the data item in question.
See “Details” for the default that is used if actions is not supplied.
an optional character value that permits the function to work with
objects that store flags in e.g. object@metadata$flags$where
instead of in object@metadata$flags, and data within
object@data$where instead of within object@data. The
default value of NULL means to look withing object@metadata
itself, and this is the default within oce. (The purpose of where
is to make oce extensible by other packages, which may choose to store
data two levels deep in the data slot.)
An optional integer specifying the degree of debugging, with
value 0 meaning to skip debugging and 1 or higher meaning to print some
information about the arguments and the data. It is usually a good idea to set
this to 1 for initial work with a dataset, to see which flags are being
handled for each data item. If not supplied, this defaults to the value of
getOption("oceDebug").
Wong, Annie, Robert Keeley, Thierry Carval, and Argo Data Management Team. "Argo Quality Control Manual for CTD and Trajectory Data," January 1, 2020. https://archimer.ifremer.fr/doc/00228/33951/.
Other functions relating to data-quality flags:
defaultFlags(),
handleFlags,adp-method,
handleFlags,ctd-method,
handleFlags,oce-method,
handleFlags,section-method,
handleFlags(),
initializeFlagScheme,ctd-method,
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 argo data:
[[,argo-method,
[[<-,argo-method,
argo-class,
argoGrid(),
argoNames2oceNames(),
argo,
as.argo(),
plot,argo-method,
read.argo(),
subset,argo-method,
summary,argo-method
# NOT RUN {
library(oce)
data(argo)
argoNew <- handleFlags(argo)
# Demonstrate replacement, looking at the second profile
f <- argo[["salinityFlag"]][,2]
df <- data.frame(flag=f, orig=argo[["salinity"]][,2], new=argoNew[["salinity"]][,2])
df[11:15,] # notice line 13
# }
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