similar to: S4 method dispatch with inheritance

Howdy all, I have a problem that I'd like some advice/help in solving---it has to do with R's pass-by-value system. I understand the issue, but am wondering if anyone has found a working solution in dealing with it for cases when one wants to modify an object inside of a method, specifically when working with S4. I'm aware that R.oo is able to deal with this using S3, but I'd

This is a Request For Comment, also BCCed to 390 package maintainers of reverse dependencies of the Matrix package. Most users and package authors working with our 'Matrix' package will be using it for numerical computations, and so will be using "dMatrix" (d : double precision) matrix objects M, and indirectly, e.g., for M >= c will also use "lMatrix" (l:

>>>>> Michael Lawrence <lawrence.michael at gene.com> >>>>> on Sun, 1 Feb 2015 19:23:06 -0800 writes: > I've implemented the proposed changes in > R-devel. Minimally tested, so please try it. It should > delegate to r/cbind2 when there is at least one S4 > argument and S3 dispatch fails (so you'll probably want to

Are you able to create a reproducible example, somehow? Thanks, Michael On Mon, Feb 9, 2015 at 2:28 PM, Mario Annau <mario.annau at gmail.com> wrote: > Hi Michael, > I've tested your change in r67699 (using r67773) and the function now > correctly dispatches to r/cbind2 within the R-session without > bind_activation(TRUE). However, running unit tests using R CMD check I

>>>>> Mario Annau <mario.annau at gmail.com> >>>>> on Wed, 11 Feb 2015 20:18:53 +0100 writes: > sorry - I just got irritated by my different R-versions. > The behaviour I described in the previous mail was discovered using R > 3.1.2 without bind_activation(TRUE). In r67773 all calls are delegated > to r/cbind.matrix and not

Fine with me as long as eliminating the inconveniences associated with it can be put on the roadmap. The alias instability and the fact that the user has no way to know if s/he should do ?`foo,numeric-method` or ?`foo,numeric,ANY-method` to find the method has been a long-standing problem. H. On 3/21/19 21:29, Michael Lawrence wrote: If we started over, I'd try to avoid this sort of

I represent a graph as an adjacency matrix of class "dgCMatrix" (from the Matrix package). > xx 5 x 5 sparse Matrix of class "dgCMatrix" a b c d e a . 1 1 . . b 1 . 1 . . c 1 1 . 1 1 d . . 1 . 1 e . . 1 1 . To check if the matrix defines and undirected graph, I have made the following functions/methods: is.UG <- function (object) { UseMethod("is.UG") }

Hi All, I have tried to find an answer within documentation, but I cannot: o How can call a class "slot" without knowing the name a priori? E.g., let's say I use the "pcaMethods" library to create a "pcaRes" object. How can I call parts of that object without using the specific names of the object in the call? example code: library(pcaMethods)

>>>>> Michael Lawrence <lawrence.michael at gene.com> >>>>> on Sat, 24 Jan 2015 06:39:37 -0800 writes: > On Sat, Jan 24, 2015 at 12:58 AM, Mario Annau > <mario.annau at gmail.com> wrote: >> Hi all, this question has already been posted on >> stackoverflow, however without success, see also >>

Hi Martin, package arules heavily relies on ngCMatrix and uses multiplication and addition for logical operations. I think it makes sense that in a mixed operation with one dgCMatrix and one ngCMatrix the ngCMatrix should be "promoted" to a dgCMatrix. The current behavior of %*% and friends is in deed confusing: > m <- matrix(sample(c(0,1), 5*5, replace=TRUE), nrow=5) >

HI, The code was working perfectly fine yesterday and today, until half an hour ago.? Couldn't find any problems in the code. Still, I am getting error message. myMatrix <- data.matrix(read.table(text=" Name??????????? Age ANTONY??????? 27 IMRAN????????? 30 RAJ????????????????? 22 NAHAS????????? 32 GEO??????????????? 42 ", header=TRUE)) MinMaxArray? <- data.frame(MIN =

I have some code where the primary dispatching is on other parameters so I'd like not to have to create a set of functions for "matrix" and another duplicate set for "array". But the class union technique isn't working as implemented below and I don't have my Green book with me. How do I fix my infinite recursion problem?

I recently encountered this and was wondering if someone could explain what happened. Basis of question involves what the difference between the calls makes as the end result is the same: > identical(matrix(1:8, nrow = 1), array(1:8, c(1, 8))) TRUE If I run the code below as shown, I get the following: > foo(1:8, 4) foo (vector, numeric) val = 4 foo (matrix, ANY) val = 500 foo

I have been running into difficulties with dispatching on an S4 class defined in the SparseM package, when the method calls are inside a function passed as the f= argument to optimize() in functions in the spdep package. The S4 methods are typically defined as: setMethod("det","matrix.csr", function(x, ...) det(chol(x))^2) that is within setMethod() rather than by name before

Hello, I've been attempting to make a generic method that dispatches on the first argument, which can be either an S3 or an S4 class. This is as far as I've gotten. Any suggestions about what to try next ? library(aroma.affymetrix) library(GenomicRanges) setGeneric("analyse", function(x, y, ...) standardGeneric("analyse")) setMethodS3("analyse",

Hi, I have a dataset which has around 138 variables and 30,000 cases. I am trying to calculate a mahalanobis distance matrix for them and my procedure is like this: Suppose my data is stored in mymatrix > S<-cov(mymatrix) # this is fine > D<-sapply(1:nrow(mymatrix), function(i) mahalanobis(mymatrix, mymatrix[i,], S)) Error in solve.default(cov, ...) : system is computationally

Dear R Users, I am writing code to present my output data (I'm using Lattice Package). However, it's essential for me to control space between barchart and legend. I've read the package's specification, but unfortunately I haven't spot the information how to do this. Here's the code I've written: barchart(mymatrix[,1:ncol(mymatrix)],horizontal=FALSE,

dear r-users, i have got a problem which i am trying to solve: i have got the following commands: Mymatrix <- matrix(1:9,ncol=3) Z <- list("V1"=c("a","",""),"V2"=c("b","",""),"V3"=c("c","",""),"V4"=c("d","","")) Mymatrix <-

Loading an S4 object from a file without first loading the library sometimes (?, the example below and actual example involves a virtual base class and the show generic) leads to incorrect dispatch (to the base class method). The attached package reproduces the problem. It has setClass("A") setClass("B", contains="A") setMethod("show", "A",

In the Matrix package v. 0.995-11 I see that the dgTMatrix Class for compressed, sparse, triplet-form matrices handles Identically indexed data instances by summing their values, e.g., library(Matrix) (Mt <- new("dgTMatrix", i = as.integer(c(0,0,1,1,4)), j = as.integer(c(0,1,2,2,4)), x = as.double(1:5), Dim = as.integer(c(5,5)))) ## 5 x 5 sparse Matrix of class