Set Preference for Adjusted Values — preferAdjusted • oce

argo data can contain "adjusted" forms of data items, which may be more trustworthy than the original data, and preferAdjusted lets the user express a preference for such adjusted data. This means that using [[,argo-method on the results returned by preferAdjusted will (if possible) return adjusted data, and also use those adjusted data in computations of derived quantities such as Absolute Salinity. The preference applies also to units and to data-quality flags, both of which can be returned by [[,argo-method, as discussed in “Details”.

Usage

preferAdjusted(argo, which = "all", fallback = TRUE)

Arguments

argo: An argo object.
which: A character vector naming the items for which (depending also on the value of fallback) adjusted values are to be sought by future calls to [[,argo-method. The short names are used, e.g. which="oxygen" means that adjusted oxygen is to be returned in future calls such as argo[["oxygen"]]. The default, "all", means to use adjusted values for any item in argo that has adjusted values.
fallback: A logical value indicating whether to fall back to unadjusted values for any data field in which the adjusted values are all NA. The default value, TRUE, avoids a problem with biogeochemical fields, where adjustment of any one field may lead to insertion of "adjusted" values for other fields that consist of nothing more than NAs.

Value

An argo object its metadata slot altered (in its adjustedWhich and adjustedFallback elements) as a signal for how [[,argo-method should function on the object.

Details

preferAdjusted() merely sets two items in the metadata slot of the returned argo object. The real action is carried out by [[,argo-method but, for convenience, the details are explained here.

Consider salinity, for example. If which equals "all", or if it is a character vector containing "salinity", then using [[,argo-method on the returned object will yield the adjusted forms of the salinity data, its associated flags, or its units. Thus, in the salinity case,

argo[["salinity"]] will attempt to return argo@data$salinityAdjusted instead of returning argo@data$salinity, although if the adjusted values are all NA then, depending on the value of fallback, the unadjusted values may be returned; similarly
argo[["salinityFlags"]] will attempt to return argo@metadata$flags$salinityAdjusted instead of argo@metadata$flags$salinity, and
argo[["salinityUnits"]] will attempt to return argo@metadata$units$salinityAdjusted instead of argo@metadata$units$salinity.

The default value, which="all", indicates that this preference for adjusted values will apply to all the elements of the data slot of the returned object, along with associated flags and units. This can be handy for quick work, but analysts may also choose to restrict their use of adjusted values to a subset of variables, based on their own decisions about data quality or accuracy.

The default value fallback=TRUE indicates that later calls to [[,argo-method should return unadjusted values for any data items that have NA for all the adjusted values. This condition is rare for core variables (salinity, temperature and pressure) but is annoyingly common for biogeochemical variables; see e.g. Section 2.2.5 of Reference 1 for a discussion of the conditions under which Argo NetCDF files contain adjusted values. Setting fallback=FALSE means that adjusted values (if they exist) will always be returned, even if they are a useless collection of NA values.

Error fields, such as salinityAdjustedError, are returned as-is by [[,argo-method, regardless of whether the object was created by preferAdjusted.

It should be noted that, regardless of whether preferAdjusted has been used, the analyst can always access either unadjusted or adjusted data directly, using the original variable names stored in the source NetCDF file. For example, argo[["PSAL"]] yields unadjusted salinity values, and argo[["PSAL_ADJUSTED"]] yields adjusted values (if they exist, or NULL if they do not). Similarly, adjusted value can always be obtained by using a form like argo[["salinityAdjusted"]].

References

Argo Data Management Team. "Argo User's Manual V3.3." Ifremer, November 28, 2019. doi:10.13155/29825

Author

Dan Kelley, based on discussions with Jaimie Harbin (with respect to the [[,argo-method interface) and Clark Richards (with respect to storing the preference in the metadata slot).

Examples

library(oce)
data(argo)
argoAdjusted <- preferAdjusted(argo)
all.equal(argo[["salinityAdjusted"]], argoAdjusted[["salinity"]])
#> [1] TRUE
all.equal(argo[["salinityFlagsAdjusted"]], argoAdjusted[["salinityFlags"]])
#> [1] TRUE
all.equal(argo[["salinityUnitsAdjusted"]], argoAdjusted[["salinityUnits"]])
#> [1] TRUE