>>>>> Martin Morgan <mtmor...@fhcrc.org>
>>>>> on Fri, 02 Jul 2010 07:01:54 -0700 writes:
> On 07/02/2010 05:05 AM, Joris Meys wrote:
>> Dear all,
>>
>> I'm getting more and more frustrated with the whole S4 thing and I'm
>> looking for a more advanced summary on how to deal with them. Often I
>> get error messages that don't make sense at all, or the code is not
>> doing what I think it would do. Far too often inspecting the code
>> requires me to go to the source, which doesn't really help in easily
>> finding the bit of code you're interested in.
>>
>> Getting the code with getAnywhere() doesn't always work. Debug()
>> doesn't work. Using trace() and browser() is not an option, as I can't
>> find the correct method.
>>
>> eg :
>> library(raster)
>>> getAnywhere(xyValues)
>> A single object matching ‘xyValues’ was found
>> It was found in the following places
>> package:raster
>> namespace:raster
>> with value
>>
>> standardGeneric for "xyValues" defined from package "raster"
>>
>> function (object, xy, ...)
>> standardGeneric("xyValues")
>> <environment: 0x04daf14c>
>> Methods may be defined for arguments: object, xy
>> Use showMethods("xyValues") for currently available ones.
>>> showMethods("xyValues")
>> Function: xyValues (package raster)
>> object="Raster", xy="data.frame"
>> object="Raster", xy="SpatialPoints"
>> object="Raster", xy="vector"
>> object="RasterLayer", xy="matrix"
>> object="RasterStackBrick", xy="matrix"
>>
>> And now...?
> selectMethod(xyValues, c('RasterLayer', 'matrix'))
> would be my choice.
Yes. Alternatively, asking showMethods() to show *all*
methods directly, can sometimes
be even quicker in revealing things:
I.e.,
showMethods("xyValues", incl=TRUE)
is often
what I use.
Martin Maechler, ETH Zurich
>> Is there an overview that actually explains how you get the
>> information you're looking for without strolling through the complete
>> source? Sorry if I sound frustrated, but this is costing me huge
>> amounts of time, to that extent that I rather write a custom function
>> than use one in an S4 package if I'm not absolutely sure about what it
>> does and how it achieves it.
> I don't really have the right experience, but Chamber's 2008 Software
> for Data Analysis... and Gentleman's 2008 R Programming for
> Bioinformatics... books would be where I'd start. ?Methods and ?Classes
> are I think under-used.
> Martin
>>
>> Cheers
>> Joris
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
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