defaultFlags: Suggest a default flag vector for bad or suspicious data

View source: R/AllClass.R

defaultFlagsR Documentation

Suggest a default flag vector for bad or suspicious data


defaultFlags tries to suggest a reasonable default flag scheme for use by handleFlags(). It does this by looking for an item named flagScheme in the metadata slot of object. If flagScheme is found, and if the scheme is recognized, then a numeric vector is returned that indicates bad or questionable data. If flagScheme$default exists, then that scheme is returned. However, if that does not exist, and if flagScheme$name is recognized, then a pre-defined (very conservative) scheme is used, as listed below.





An oce object


  • for argo, the default is c(0,3,4,6,7,9), meaning to act upon not_assessed (0), probably_bad (3), bad (4), not_used_6 (6), not_used_7 (7) and missing (9). See Section 3.2.2 of Carval et al. (2019).

  • for BODC, the default is c(0,2,3,4,5,6,7,8,9), i.e. all flags except good.

  • for DFO, the default is c(0,2,3,4,5,8,9), i.e. all flags except appears_correct.

  • for ⁠WHP bottle⁠, the default is c(1,3,4,5,6,7,8,9), i.e. all flags except no_problems_noted.

  • for ⁠WHP ctd⁠, the default is c(1,3,4,5,6,7,9), i.e. all flags except acceptable.


A vector of one or more flag values, or NULL if object metadata slot lacks a flagScheme as set by initializeFlagScheme(), or if it has a scheme that is not in the list provide in “Description”.


  • Carval, Thierry, Bob Keeley, Yasushi Takatsuki, Takashi Yoshida, Stephen Loch Loch, Claudia Schmid, and Roger Goldsmith. Argo User's Manual V3.3. Ifremer, 2019. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.13155/29825")}

See Also

Other functions relating to data-quality flags: handleFlags,adp-method, handleFlags,argo-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()

oce documentation built on April 25, 2023, 5:07 p.m.