R: Deprecated and Defunct Elements of package 'oce'

oce-deprecated {oce} | R Documentation

## Deprecated and Defunct Elements of package ‘oce’

### Description

Certain functions and function arguments are still provided for compatibility with older versions of ‘oce’, but will be removed soon. The ‘oce’ scheme for removing functions is similar to that used by ‘Bioconductor’: items are marked as "deprecated" in one release, as "defunct" in the next, and then removed entirely. This goal is to provide a gentle migration path for users who keep their packages reasonably up-to-date.

### Details

Several ‘oce’ functions are marked "deprecated" in the present release of oce. Please use the replacement functions as listed below.

Deprecated | Replacement | Notes
`mapZones` | `mapGrid` | Improve name sensibility
`mapMeridians` | `mapGrid` | Improve name sensibility
`addColumn` | `oceSetData` | Deprecated 2016-08-01
`oce.magic` | `oceMagic` | Deprecated 2016-09-01
`ctdAddColumn` | `oceSetData` | Deprecated 2016-11-11
`ctdUpdateHeader` | - | Deprecated 2016-11-11

The next CRAN release of ‘oce’ will have these functions flagged as "defunct", which will mean that trying to use them will generate an error and a hint as to the replacement function.

The following are marked "defunct", which means that calling them in the present version of oce will produce an error, and that they will be removed altogether in the next oce release on CRAN.

Defunct | Replacement | Notes
`makeSection` | `as.section` | Improve utility and name sensibility
`columns` | `read.ctd` | Unnecessary, and never worked

Several ‘oce’ function arguments are considered defunct, which means they will be removed in the next CRAN release. They are as follows.

- The `date` argument of `as.ctd` was discovered to have been unused in early 2016. Since the `startTime` actually fills its role, `date` was considered to be deprecated in June 2016.

- The `quality` flag of `as.ctd` was marked as deprecated in March 2016.

- The `fill` argument of `mapPlot` was confusing to users, so it was designated as deprecated in June 2016. (The confusion stemmed from subtle differences between `plot` and `polygon`, and the problem is that `mapPlot` can use either of these functions, according to whether coastlines are to be filled.) The functionality is preserved, in the `col` argument.

- The `adorn` argument of `plot,ctd-method` and other functions was realized in June 2016 to be dangerous. (If the adornment code contained assignments to temporary variables, there could be conflicts with the plotting code. The only way to be sure of not overriding an important variable would be to understand the full plotting code, which is far too demanding to justify.) The solution is for users to draw panels individually, adding graphical elements with conventional R functions such as `lines`, etc.

### See Also

The ‘Bioconductor’ scheme for removing functions is described at https://www.bioconductor.org/developers/how-to/deprecation/ and it is extended here to function arguments.

[Package oce version 0.9-20 Index]