handleFlags,section-method {oce} | R Documentation

## Handle flags in Section 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 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.

### Usage

    ## S4 method for signature 'section'
    handleFlags(object, flags = list(), actions = list(),
      debug = integer())

### Arguments

`object` | An object of `section-class`.

`flags`

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. See “Details” for the default that is used if `flags` is not supplied.

`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")`.

### Details

If `flags` and `actions` are not provided, the default is to use WHP (World Hydrographic Program) flags [1], in which the value 2 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 WHP flag codes run from 1 to 9, this default is equivalent to setting `flags=list(all=c(1, 3:9))` along with `action=list("NA")`.

### References

1. https://www.nodc.noaa.gov/woce/woce_v3/wocedata_1/whp/exchange/exchange_format_desc.htm

### See Also

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

Other things related to `section` data: `[[,section-method`, `[[<-,section-method`, `as.section`, `plot,section-method`, `read.section`, `section-class`, `sectionAddStation`, `sectionGrid`, `sectionSmooth`, `sectionSort`, `section`, `subset,section-method`, `summary,section-method`

### Examples

    library(oce)
    data(section)
    section2 <- handleFlags(section)
    par(mfrow=c(2, 1))
    plotTS(section)
    plotTS(section2)

[Package oce version 0.9-22 Index]