applyQC: Apply Quality Control Flags

Description Usage Arguments Details Value Author(s) References Examples

View source: R/qc.R

Description

This function examines the quality-control ("QC") flags within an argoFloats object that was created by readProfiles(). By default, it replaces all suspicious data with NA values, so they will not appear in plots or be considered in calculations. This is an important early step in processing, because suspicious Argo floats commonly report data that are suspicious based on statistical and physical measures, as is illustrated in the “Examples” section. See section 3.3 of Kelley et al. (2021) for more on this function.

Usage

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applyQC(x, flags = NULL, actions = NULL, debug = 0)

Arguments

x

an argoFloats object of type "argos", as created by readProfiles().

flags

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 NULL then flags=list(c(0,3,4,6,7,9)) is used by default where: 0 = data that have not yet been assessed, 3 = "probably bad" data, 4 = for "bad" data, 6 = an unused flag, 7 = an unused flag, or 9 = "missing" data.

See Sections 3.2.1 and 3.2.2 of Carval et al. (2019) for more information on these QC code values.

actions

the actions to perform. The default, NULL, means to use the actions set up by readProfiles(), which, by default. causes any data flagged as suspicious to be set to NA.

debug

an integer passed to oce::handleFlags,argo-method(). If this is set to a positive value, then some debugging information will be printed as the processing is done.

Details

The work is done by using oce::handleFlags,argo-method() on each of the profiles stored within the object. In most cases, only the object needs to be specified, for the default actions coincide with common conventions for flags in Argo data.

Value

A copy of x but with each of the objects within its data slot having been passed through oce::handleFlags,argo-method().

Author(s)

Dan Kelley

References

Carval, Thierry, Bob Keeley, Yasushi Takatsuki, Takashi Yoshida, Stephen Loch, Claudia Schmid, and Roger Goldsmith. Argo User's Manual V3.3. Ifremer, 2019. doi:10.13155/29825

Kelley, D. E., Harbin, J., & Richards, C. (2021). argoFloats: An R package for analyzing Argo data. Frontiers in Marine Science, (8), 636922. doi: 10.3389/fmars.2021.635922

Examples

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# Demonstrate applyQC to a built-in file
library(argoFloats)
f <- system.file("extdata", "SR2902204_131.nc", package="argoFloats")
raw <- readProfiles(f)
clean <- applyQC(raw)
oldpar <- par(no.readonly=TRUE)
par(mar=c(3.3, 3.3, 1, 1), mgp=c(2, 0.7, 0))
plot(raw, col="red", which="TS")
points(clean[[1]][["SA"]], clean[[1]][["CT"]], pch=20)
legend("topleft", pch=20, cex=1,
    col=c("black", "red"), legend=c("OK", "Flagged"), bg="white")
par(oldpar)

dankelley/argoFloats documentation built on Oct. 19, 2021, 1:17 p.m.