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, marked as "defunct" in the next, and removed in the next after that. 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. The next CRAN release of ‘oce’ will designate these functions as "defunct".

Deprecated | Replacement | Notes
`mapZones` | `mapGrid` | Deprecated 2016-02-13
`mapMeridians` | `mapGrid` | Deprecated 2016-02-13
`addColumn` | `oceSetData` | Deprecated 2016-08-01
`oce.magic` | `oceMagic` | Deprecated 2016-09-01
`ctdAddColumn` | `oceSetData` | Deprecated 2016-11-11
`ctdUpdateHeader` | - | Deprecated 2016-11-11
`oce.as.POSIXlt` | `parse_date_time` | Deprecated 2016-12-17

The following are marked "defunct", so calling them in the the present version produces an error message that hints at a replacement function. Once a function is marked "defunct" on one CRAN release, it will be slated for outright deletion in a subsequent release.

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

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

- The `endian` argument of `byteToBinary` will be removed sometime in the year 2017, and should be set to `"big"` in the meantime.

- The `parameters` argument of `plot,ctd-method` was deprecated on 2016-12-30. It was once used by `plot,coastline-method` but has been ignored by that function since February 2016.

- The `orientation` argument of `plot,ctd-method` was deprecated on 2016-12-30. It was once used by `plot,coastline-method` but has been ignored by that function since February 2016.

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 0.9-22 Index]