R: Establish a data-quality scheme for a oce object

initializeFlagScheme {oce} | R Documentation

## Establish a data-quality scheme for a oce object

### Description

This function stores add an item named `flagScheme` to the `metadata` slot of an object inheriting from `oce-class`. This is a list containing two items: `name` and `mapping`, as provided in the function arguments. The purpose is both to document a flag scheme and to make it so that `initializeFlags`, `setFlags` and `handleFlags` can specify flags by name, as opposed to number. This is a generic function, that may be specialized to the class of `object` (see “Details”).

### Usage

    initializeFlagScheme(object, name = NULL, mapping = NULL, debug = 0)

### Arguments

`object` | An oce object.
`name` | Character value naming the scheme. If this refers to a pre-defined scheme, then `mapping` must not be provided.
`mapping` | A list of named items describing the mapping from flag meaning to flag numerical value, e.g `list(good=1, bad=2)` might be used for a hypothetical class.
`debug` | Integer set to 0 for quiet action or to 1 for some debugging.

### Details

The following pre-defined schemes are available (note that the names are simplified from the phrases used in defining documentation):

- `name="argo"` defaults `mapping` to `list(not_assessed=0, passed_all_tests=1, probably_good=2, probably_bad=3, bad=4, averaged=7, interpolated=8, missing=9)`. See [1] for a deeper explanation of the meanings of these codes.

- `name="BODC"` defaults `mapping` to `list(no_quality_control=0, good=1, probably_good=2, probably_bad=3, bad=4, changed=5, below_detection=6, in_excess=7, interpolated=8, missing=9)`. See [2] for a deeper explanation of the meanings of these codes, and note that codes `A` and `Q` are not provided in oce.

- `name="DFO"` defaults `mapping` to `list(no_quality_control=0, appears_correct=1, appears_inconsistent=2, doubtful=3, erroneous=4, changed=5, qc_by_originator=8, missing=9)`. See [3] for a deeper explanation of the meanings of these codes.

- `name="WHP bottle"` defaults `mapping` to `list(no_information=1, no_problems_noted=2, leaking=3, did_not_trip=4, not_reported=5, discrepency=6, unknown_problem=7, did_not_trip=8, no_sample=9)`. See [4] for a deeper explanation of the meanings of these codes.

- `name="WHP CTD"` defaults `mapping` to `list(not_calibrated=1, acceptable=2, questionable=3, bad=4, not_reported=5, interpolated=6, despiked=7, missing=9)`. See [4] for a deeper explanation of the meanings of these codes.

### Value

An object with the `metadata` slot containing `flagScheme`.

### Caution

This function was added in early May, 2018, and is likely to undergo changes until the autumn of that year. Use with caution.

### References

1. The codes for `"Argo"` are defined at http://www.oceannetworks.ca/data-tools/data-quality

2. The codes for `"BODC"` are defined at http://seadatanet.maris2.nl/v_bodc_vocab_v2/browse.asp?order=conceptid&formname=search&screen=0&lib=l20

3. The codes for `"DFO"` are defined at http://www.dfo-mpo.gc.ca/science/data-donnees/code/list/014-eng.html

4. The codes for `"WHP CTD"` and `"WHP bottle"` are defined at https://www.nodc.noaa.gov/woce/woce_v3/wocedata_1/whp/exchange/exchange_format_desc.htm

### See Also

Other functions relating to data-quality flags: `defaultFlags`, `handleFlags,adp-method`, `handleFlags,argo-method`, `handleFlags,ctd-method`, `handleFlags,section-method`, `handleFlags`, `initializeFlagScheme,ctd-method`, `initializeFlagScheme,oce-method`, `initializeFlagScheme,section-method`, `initializeFlags,adp-method`, `initializeFlags,oce-method`, `initializeFlags`, `setFlags,adp-method`, `setFlags,ctd-method`, `setFlags,oce-method`, `setFlags`

Other things related to `oce` data: `initializeFlagScheme,oce-method`

[Package oce version 1.0-1 Index]