similar to: extending data.frame with S4 class

Dear R Programmers! After some time of using R I decided to work through John Chambers book "Programming with Data" to learn what these S4 classes are all about and how they work in R. (I regret not having picked up this rather fine book earlier!) I know from the documentation and the mailing archives that S4 in R is not 100% the book and that there are issues especially with

One of the changes some packages are noticing from the recent modifications to methods is warnings of "undefined classes" during installation when the package extends S3 classes or uses them as slots UNLESSS they have been declared in a setOldClass() call. The green book "strongly recommends" declaring S3 classs this way (pp 449-451). The warnings on undeclared classes

On 05/28/2015 02:49 AM, Julien Id? wrote: > Hey everyone, > > I would like to develop a package using S4 classes. > I have to define several S4 classes that inherits from each others as > follow: > > # A <- B <- C <- D > > I also would like to define .DollarNames methods for these class so, if I > have understood well, I also have to define an old class as

Up to now, writing an S4 class that extends an S3 class (using contains= in the call to setClass) has been discouraged for two main reasons: 1. You can't say anything formal about S3 classes, so validating objects, having formal slots for their properties, etc. are not generally feasible. 2. In any case, the S3 class, which may have multiple strings in the class attribute, was not

Hey everyone, I would like to develop a package using S4 classes. I have to define several S4 classes that inherits from each others as follow: # A <- B <- C <- D I also would like to define .DollarNames methods for these class so, if I have understood well, I also have to define an old class as follow: # AOld <- A <- B <- C <- D setOldClass(Classes = "AOld")

r-devel, In a development version of the CRAN package metrumrg, I write ... require(reshape) setGeneric('cast') setOldClass(c('keyed','data.frame')) setMethod('cast','keyed', function ...) The result is satisfactory when sourcing the code directly, but when checking the package (which has 'reshape' as a dependency in the DESCRIPTION file) I get

Hello, I am the maintainer of the stringkernels package and have come across a problem with using S3 objects in my S4 classes. Specifically, I have an S4 class with a slot that takes a text corpus as a list of character vectors. tm (version 0.5) saves corpora as lists with a class attribute of c("VCorpus", "Corpus", "list"). I don't actually need the

Hi all, I am having a problem trying to declare a slot representation to hold a file connection. With V2.8.0 I had been using: setClass("Element", representation( [other slots removed], datafileConn = setOldClass(c("file","connection")) ) ) This resulted in a warning but still ran okay. No however with V2.9.0 I am getting

Hi all, this is my first post in R devel? sorry if I lost some of the guidelines. Anyway this is my problem: Version: R version 2.15.2 (2012-10-26) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) I want to make an S4 class that use the output object of the function of nls.lm as a slot: setOldClass("nls.lm") setClass ( Class="TestClass",

Hi, I'm trying to make a new S4 object with a slot for a "link-glm" object. R doesn't like me have a slot of class "link-glm" > class(make.link("probit")) [1] "link-glm" > setClass("a",representation(item="link-glm")) [1] "a" Warning message: undefined slot classes in definition of "a": item(class

>>>>> Herv? Pag?s <hpages at fredhutch.org> >>>>> on Tue, 12 May 2015 15:18:42 -0700 writes: > Hi, > The man page for new() suggests that if 'a' is an object with slots > "slot1" and "slot2" and C is a class that extends the class of 'a', > then the 2 following calls should be equivalent: >

Dear listmembers, I would like to define a class with a slot that takes either an object of class aov or NULL. I have been reading "S4 Classes in 15 pages more or less" and "Lecture: S4 classes and methods" #First I tried with list and NULL setClass(listOrNULL") setIs("list", "listOrNULL") setIs("NULL", "listOrNULL") #doesn't

Hi, I realize this is an old thread, but just wondering whether a conclusion was ever reached on this issue? I'm using formula(NULL) but it would be nice if default initialization worked for formula classes as well. Cheers, Josh On Thu, May 14, 2015 at 8:13 AM, Herv? Pag?s <hpages at fredhutch.org> wrote: > Thanks Martin for looking into this. H. > > > On 05/13/2015

Answering to convey the 'rules' as I know them, rather than to address the underlying issues that I guess you are really after... The S4 practice is to use setOldClass() to explicitly treat an S3 character() vector of classes as an assertion of linear inheritance > x <- structure (sqrt (37), class = c ("sqrt.prime", "numeric") ) > is(x,

I'm trying to create an extension to data.frame with more complex row and column names, and have run into some problems: > setClass("new-data.frame", representation("data.frame")) [1] "new-data.frame" Warning message: old-style ('S3') class "data.frame" supplied as a superclass of "new-data.frame", but no automatic conversion will

>>>>> Joshua Wiley <jwiley.psych at gmail.com> >>>>> on Thu, 8 Oct 2015 12:19:16 +1100 writes: > Hi, I realize this is an old thread, but just wondering > whether a conclusion was ever reached on this issue? I'm > using formula(NULL) but it would be nice if default > initialization worked for formula classes as well. Well,

Is there a conventional way to test for nested factors? I.e., if 'a' and 'b' are lists of same-length factors, does each level specified by 'a' correspond to exactly one level specified by 'b'? The function below seems to suffice, but I'd be happy to know of a more succinct solution, if it already exists. Thanks, Tim. --- "%nested.in%" <-

Thanks Martin for looking into this. H. On 05/13/2015 03:57 AM, Martin Maechler wrote: >>>>>> Herv? Pag?s <hpages at fredhutch.org> >>>>>> on Tue, 12 May 2015 15:18:42 -0700 writes: > >> Hi, > >> The man page for new() suggests that if 'a' is an object with slots >> "slot1" and "slot2" and C is a

Suppose I have a list of logicals, such as returned by lapply: Theoph$Dose[1] <- NA Theoph$Time[2] <- NA Theoph$conc[3] <- NA lapply(Theoph,is.na) Is there a direct way to execute logical "or" across all vectors? The following gives the desired result, but seems unnecessarily complex. as.logical(apply(do.call("rbind",lapply(Theoph,is.na)),2,"sum"))

I am new to using S4 methods and have run into this problem (on Windows XP using R 2.4.1): I am writing a package in which I use the graph package. I define my own classes of graphs as: setOldClass("graphsh") setOldClass("ugsh") setIs("ugsh", "graphsh") (I know that I "should have" used setClass instead - and I will eventually - but right now