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.
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 the following 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 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.
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.