Dear Gavin,
unfortunately, I cannot overwrite plot.data.frame only. If I do this I
get the following warning from R CMD check:
* checking use of S3 registration ... WARNING
Registered S3 method from a standard package overwritten by 'papeR':
method from
plot.data.frame graphics
The reason for this is given in the following statement by Prof. Ripley:
> Do not replace registered S3 methods from base/recommended packages,
> something which is not allowed by the CRAN policies and will mean
> that everyone gets your method even if your namespace is unloaded.
The route I am taking is one of the advised routes to go (see
https://github.com/hofnerb/papeR/issues/5). So I am still looking for a
fix of this issue.
Your warning regarding the changed user experience is well noted.
However, I think (and am aware that this is my personal opinion) that a
lot of users will not miss the standard plot.data.frame method which is
only well defined for numerics anyway and not very informative in many
situations. After your comment I am thinking of adding an option to my
plot.data.frame function which allows to fall back to the original user
experience.
Thanks,
Benjamin
Am 01.09.2015 um 04:37 schrieb Gavin Simpson:
Why do you even need to take over `plot`, `plot.default`? You can just
register/export the plot.data.frame method from our package without
touching the generic or default method. The part of WRE that you refer
to is about making functions that are *not* S3 methods in one of base R
or it's packages into S3 generics. You are just providing a method for
an existing generic so you don't need to follow that code.
That said, it wouldn't be good form to fundamentally alter the way
plot.data.frame worked as users might expect certain functionality.
HTH
G
On 31 August 2015 at 04:03, Benjamin Hofner <benjamin.hof...@fau.de
<mailto:benjamin.hof...@fau.de>> wrote:
Dear all,
CRAN policies do not allow that single methods (for generic
functions) which are defined in base or recommended packages are
replaced. They advice package authors to replace the standard
generic and use a xxx.default method which then calls the original
standard generic.
Using the following code
## overwrite standard generic
plot <- function(x, y, ...)
UseMethod("plot")
## per default fall back to standard generic
plot.default <- function(x, y, ...)
graphics::plot(x, y, ...)
## now specify modified plot function for data frames
plot.data.frame <- function(x, variables = names(x), ...)
essentially works for all tested plot.xxx functions. Yet, it breaks
plot.formula. How can I proceed to overwrite plot.data.frame without
breaking plot.formula. Any help is greatly appreciated.
For a detailed description of the problem with syntax highlighting
and code to reproduce the problem please see:
http://stackoverflow.com/questions/32246361/redefinition-of-generic-for-plot-function-breaks-plot-formula
Best,
Benjamin
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Dr. rer. nat. Benjamin Hofner
Institut für Medizininformatik, Biometrie und Epidemiologie
Friedrich-Alexander-Universität Erlangen-Nürnberg
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http://www.benjaminhofner.de
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