Handle Flags in ARGO Objects


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 mached data.

Reasonable defaults are used if flags and actions are not supplied (see ‘Details’), but different schemes are used in different data archives, so it is risky to rely on these defaults. It is usually necessary to tailor flags and actions to the data and the analysis goals.


## S4 method for signature 'argo'
handleFlags(object, flags = list(), actions = list())



An object of argo-class.


An optional list containing (a) items with names of entries in the data slot of object, or (b) a single unnamed item. In the first case, the attention is focussed on the named items, while in the second case the all the data in the object's data slot are examined. Each element in the list must be set to an integer or vector of integers, specifying conditions to be met before actions are to be taken.


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.


If flags and actions are not provided, the default is to use ARGO flags [1], in which the value 1 indicates good data, and other values indicate either unchecked, suspicious, or bad data. Any data not flagged as good are set to NA in the returned value. Since Argo flag codes run from 0 to 4, this default is equivalent to setting flags=list(c(0, 2:4)) along with actions=list("NA").

Implementation status

handleFlags is a new function as of March 2016, and it will probably change through the Spring of 2016. Almost nothing works yet, and users should not be doing any more than looking at the documentation and telling the developers whether the planned functioning seems reasonable. The hope is to get trial code working for ctd and argo data types by the end of April. After that, there will likely be a month or more of testing with real-world work, with possible changes to the user interface. Then other types will be added, as needed.


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

See Also

Other functions that handle data-quality flags: handleFlags,ctd-method, handleFlags,section-method, handleFlags

Other things related to argo data: [[,argo-method, [[<-,argo-method, argo-class, argoGrid, argo, as.argo, plot,argo-method, read.argo, subset,argo-method, summary,argo-method


## Not run: 
# 1. Default: anything not flagged as 1 is set to NA, to focus
# solely on 'good', in the Argo scheme.
argoNew <- handleFlags(argo)

# 2. A less restrictive case: include also 'questionable' data,
# and only apply this action to salinity.
argoNew <- handleFlags(argo, flags=list(salinity=4))

## End(Not run)

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