R: Handle Flags in ARGO Objects

handleFlags,argo-method {oce}

R Documentation

Handle Flags in ARGO Objects

Description

Data-quality flags are stored in the metadata slot of oce-class 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 core data based on the data-quality flags. For example, a common operation is to replace suspicious or erroneous data with NA.

If metadata$flags in the object supplied as the first argument is empty, then that object is returned, unaltered. Otherwise, handleFlags analyses the data-quality flags within the object, in relation to the flags argument, and interprets the action argument to select an action to be applied to matched data.

Usage

## S4 method for signature 'argo'
handleFlags(object, flags = NULL, actions = NULL,
  debug = getOption("oceDebug"))

Arguments

`object`	An object of `argo-class`.
`flags`	A `list` specifying flag values upon which actions will be taken. This can take two forms. In the first, the list has named elements each containing a vector of integers. For example, salinities flagged with values of 1 or 3 through 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 with unnamed vectors, and this means to apply the actions to all the data entries; thus, `flags=list(c(1,3:9))` means to apply not just to salinity and temperature, but also to everything else that is in the `data` slot. If `flags` is not provided, then `defaultFlags` is called, to try to determine a conservative default.
`actions`	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.
`debug`	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")`.

Author(s)

Dan Kelley

References

1. http://www.argo.ucsd.edu/Argo_date_guide.html#dmodedata

Examples

library(oce)
data(argo)
# 1. Default: set to NA any data that is not flagged with
# code value 1 (meaning \code{"passed_all_tests"})
argoNew <- handleFlags(argo, flags=c(0, 2:9))
# Demonstrate replacement, looking at the second profile
f <- argo[["salinityFlag"]][,2] # first column with a flag=4 entry
df <- data.frame(flag=f, orig=argo[["salinity"]][,2], new=argoNew[["salinity"]][,2])
df[11:15,] # notice line 13

# 2. A less restrictive case: focussing just on salinity,
# retain only data with flags 1 (meaning \code{"passed_all_tests"})
# and 2 (\code{"probably_good"}).
argoNew <- handleFlags(argo, flags=list(salinity=c(0, 3:9)))

[Package oce version 1.0-1 Index]