Please read the proto vignette before asking further questions about it. It is an alternative to/version of OOP different from S3 and S4.
-- Bert On Fri, Aug 9, 2013 at 8:13 AM, Simon Zehnder <szehn...@uni-bonn.de> wrote: > Hi Martin, > > is proto in S3? > > I will take a look first at the simple package EBImage. > > Thank you very much for the suggestions! > > Best > > Simon > > > On Aug 9, 2013, at 5:01 PM, Martin Morgan <mtmor...@fhcrc.org> wrote: > >> On 08/09/2013 07:45 AM, Bert Gunter wrote: >>> Simon: >>> >>> Have a look at the "proto" package for which there is a vignette. You >>> may find it suitable for your needs and less intimidating. >> >> Won't help much with S4, though! Some answers here >> >> http://stackoverflow.com/questions/5437238/which-packages-make-good-use-of-s4-objects >> >> including from Bioconductor simple class in EBImage, the advanced IRanges >> package and the 'toy' StudentGWAS. >> >> Martin >> >>> >>> Cheers, >>> Bert >>> >>> On Fri, Aug 9, 2013 at 7:40 AM, Simon Zehnder <szehn...@uni-bonn.de> wrote: >>>> Hi Martin, >>>> >>>> thank you very much for this profound answer! Your added design advice is >>>> very helpful, too! >>>> >>>> For the 'simple example': Sometimes I am still a little overwhelmed from a >>>> certain setting in the code and my ideas how I want to handle a process. >>>> But I learn from session to session. In future I will also span the lines >>>> more than 80 columns. I am used to the indent in my vim editor. >>>> >>>> I have one further issue: I do know, that you are one of the leading >>>> developers of the bioconductor package which uses (as far as I have read) >>>> extensively OOP in R. Is there a package you could suggest to me to learn >>>> from by reading and understanding the code? Where can I find the source >>>> code? >>>> >>>> Best >>>> >>>> Simon >>>> >>>> >>>> On Aug 8, 2013, at 10:00 PM, Martin Morgan <mtmor...@fhcrc.org> wrote: >>>> >>>>> On 08/04/2013 02:13 AM, Simon Zehnder wrote: >>>>>> So, I found a solution: First in the "initialize" method of class C >>>>>> coerce >>>>>> the C object into a B object. Then call the next method in the list with >>>>>> the >>>>>> B class object. Now, in the "initialize" method of class B the object is >>>>>> a B >>>>>> object and the respective "generateSpec" method is called. Then, in the >>>>>> "initialize" method of C the returned object from "callNextMethod" has >>>>>> to be >>>>>> written to the C class object in .Object. See the code below. >>>>>> >>>>>> setMethod("initialize", "C", function(.Object, value) {.Object@c <- >>>>>> value; >>>>>> object <- as(.Object, "B"); object <- callNextMethod(object, value); >>>>>> as(.Object, "B") <- object; .Object <- generateSpec(.Object); >>>>>> return(.Object)}) >>>>>> >>>>>> This setting works. I do not know though, if this setting is the "usual" >>>>>> way >>>>>> such things are done in R OOP. Maybe the whole class design is >>>>>> disadvantageous. If anyone detects a mistaken design, I am very thankful >>>>>> to >>>>>> learn. >>>>> >>>>> Hi Simon -- your 'simple' example is pretty complicated, and I didn't >>>>> really follow it in detail! The code is not formatted for easy reading >>>>> (e.g., lines spanning no more than 80 columns) and some of it (e.g., >>>>> generateSpec) might not be necessary to describe the problem you're >>>>> having. >>>>> >>>>> A good strategy is to ensure that 'new' called with no arguments works >>>>> (there are other solutions, but following this rule has helped me to keep >>>>> my classes and methods simple). This is not the case for >>>>> >>>>> new("A") >>>>> new("C") >>>>> >>>>> The reason for this strategy has to do with the way inheritance is >>>>> implemented, in particular the coercion from derived to super class. >>>>> Usually it is better to provide default values for arguments to >>>>> initialize, and to specify arguments after a '...'. This means that your >>>>> initialize methods will respects the contract set out in ?initialize, in >>>>> particular the handling of unnamed arguments: >>>>> >>>>> ...: data to include in the new object. Named arguments >>>>> correspond to slots in the class definition. Unnamed >>>>> arguments must be objects from classes that this class >>>>> extends. >>>>> >>>>> I might have written initialize,A-method as >>>>> >>>>> setMethod("initialize", "A", function(.Object, ..., value=numeric()){ >>>>> .Object <- callNextMethod(.Object, ..., a=value) >>>>> generateSpec(.Object) >>>>> }) >>>>> >>>>> Likely in a subsequent iteration I would have ended up with (using the >>>>> convention that function names preceded by '.' are not exported) >>>>> >>>>> .A <- setClass("A", representation(a = "numeric", specA = "numeric")) >>>>> >>>>> .generateSpecA <- function(a) { >>>>> 1 / a >>>>> } >>>>> >>>>> A <- function(a=numeric(), ...) { >>>>> specA <- .generateSpecA(a) >>>>> .A(..., a=a, specA=specA) >>>>> } >>>>> >>>>> setMethod(generateSpec, "A", function(object) { >>>>> .generateSpecA(object@a) >>>>> }) >>>>> >>>>> ensuring that A() returns a valid object and avoiding the definition of >>>>> an initialize method entirely. >>>>> >>>>> Martin >>>>> >>>>>> >>>>>> Best >>>>>> >>>>>> Simon >>>>>> >>>>>> >>>>>> On Aug 3, 2013, at 9:43 PM, Simon Zehnder <simon.zehn...@googlemail.com> >>>>>> wrote: >>>>>> >>>>>>> setMethod("initialize", "C", function(.Object, value) {.Object@c <- >>>>>>> value; >>>>>>> .Object <- callNextMethod(.Object, value); .Object <- >>>>>>> generateSpec(.Object); return(.Object)}) >>>>>> >>>>>> ______________________________________________ R-help@r-project.org >>>>>> mailing >>>>>> list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the >>>>>> posting >>>>>> guide http://www.R-project.org/posting-guide.html and provide commented, >>>>>> minimal, self-contained, reproducible code. >>>>>> >>>>> >>>>> >>>>> -- >>>>> 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 >>>> >>>> ______________________________________________ >>>> R-help@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/r-help >>>> PLEASE do read the posting guide >>>> http://www.R-project.org/posting-guide.html >>>> and provide commented, minimal, self-contained, reproducible code. >>> >>> >>> >> >> >> -- >> 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 > -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
