search for: slotnames

Dear R experts, I have defined a class "myclass" and would like the slots to be extractable not only by "@" but also by "$". I now try to write a method for "$" that simply executes the request object at slotname, whenever someone calls object$slotname for any object of class "myclass". I don't manage to find out how I can provide this

...eed a method to convert this class forth and back into a single row data.frame, where every slots represents a column. This method looks at the moment like this: > setMethod("as.data.frame", "Transaction", function(x, row.names = NULL, optional = FALSE, ...){ slotnames <- slotNames(x) slotlist <- data.frame(rbind(1:length(slotnames))) names(slotlist) <- slotnames for(i in slotnames) { slotlist[1, i] <- slot(x, i) } return(slotlist) } ) This method doesn't require predetermined slotnames...

Hi, It's nice to be able to define S4 classes with slots that correspond to standard attributes: setClass("A1", slots=c(names="character")) setClass("A2", slots=c(dim="integer")) setClass("A3", slots=c(dimnames="list")) By doing this, one gets a few methods for free: a1 <- new("A1", names=letters[1:3])

...ottom-up quick glance only read last paragraph) to get NULL from invalid slotname. This is in reference to writing method that might be passed an object created by previous version of software, and new slots were added to class in later revisions. For such situations, is the norm then to do "slotNames(obj) %in% <slotname>" prior to accessing any slotname from extended class? TIA R version 2.7.0 Patched (2008-06-04 r45830) ---------------------------------------------------------- SIGSIG -- signature too long (core dumped)

...LIST > setClass( 'inheritList', contains='list') [1] "inheritList" > inList <- new( 'inheritList' ) > class( inList ) [1] "inheritList" attr(,"package") [1] ".GlobalEnv" > is.list( inList ) # TRUE [1] TRUE > slotNames(inList) # ".Data" [1] ".Data" > inherits(inList, 'list' ) # TRUE [1] TRUE > > > # ENVIRONMENT > setClass( 'inheritEnv', contains='environment' ) Defining type "environment" as a superclass via class ".environment&qu...

...rollable by 'test' argument) when retrieving a non-existent slot. The offending line of code is shown below: > validObject function (object, test = FALSE, complete = FALSE) { ... for (i in seq_along(slotTypes)) { classi <- slotTypes[[i]] sloti <- slot(object, slotNames[[i]]) # offending line of code One potential patch is to substitute the offending line with sloti <- try(slot(object, slotNames[[i]]), silent = TRUE) if (class(sloti) == "try-error") { errors <- c(errors, paste("missing slot \"", slotName...

...ersion: 1.9.1 OS: Windows XP Submission from: (NULL) (171.64.102.199) It would be nice if names(obj) would give slot names as well. Since for many people slots are new, the first thing that happens is you try to access what's in them and can't find how to do it. If you don't know that slotNames() exists, it can be very frustrating. Moreover, if you don't even know that the objects has slots (or that such things exist), it's extremely confusing. It just looks like nothing is there (you get NULL). If needed, you could have a message that says that these are slots and should be acces...

...ains="DataFrame", ## representation(states="StatesORNULL")) ## R> foo <- occupancy(pooledMethSegs) R> plotOccupancy(foo) Error in slot(object, "states") : no slot of name "states" for this object of class "Occupancy" R> slotNames(foo) [1] "states" "rownames" "nrows" "listData" [5] "elementType" "elementMetadata" "metadata" R> foo@states Error: no slot of name "states" for this object of class "Occupancy&quot...

...ains="DataFrame", ## representation(states="StatesORNULL")) ## R> foo <- occupancy(pooledMethSegs) R> plotOccupancy(foo) Error in slot(object, "states") : no slot of name "states" for this object of class "Occupancy" R> slotNames(foo) [1] "states" "rownames" "nrows" "listData" [5] "elementType" "elementMetadata" "metadata" R> foo@states Error: no slot of name "states" for this object of class "Occupancy&quot...

I've fixed this and will commit soon. Disregard my dim<-() example; that behaves as expected (the class needs a dim<-() method). Michael On Tue, Jun 6, 2017 at 5:16 AM, Michael Lawrence <michafla at gene.com> wrote: > Thanks for the report. The issue is that one cannot set special attributes > like names, dim, dimnames, etc on S4 objects. I was aready working on this >

When passing a list as an argument to a function, I find it convenient to attach it in the first line of th function code, then refer to the components as A, B, etc. rather than as list$A, list$B, etc. If I pass a S4 class object, is there a way to "attach" it, or do I have to refer to the slots as object at A, objetc at B, etc.? I could always make copies, A <- object at A

Thanks for the report. The issue is that one cannot set special attributes like names, dim, dimnames, etc on S4 objects. I was aready working on this and will have a fix soon. > a2 <- new("A2") > dim(a2) <- c(2, 3) Error in dim(a2) <- c(2, 3) : invalid first argument On Mon, Jun 5, 2017 at 6:08 PM, Herv? Pag?s <hpages at fredhutch.org> wrote: > Hi, > >

I created some S4 objects that are essentially data frame objects. The S4 object definitions were necessary to verify data integrity and force a standardized data format. I am, however, finding myself redefining all the typical generic functions so that I can still manipulate my S4 objects as if they were data frames ... I have used setMethod to set methods for "subset",

I want to loop through slots of an S4 object and am unsure how to do so since the only way I can find to access them is individually in the form 'object@slotName'. I have guessed at a few possibilities which did not work and I have read some S4 object tutorials and things but still unsuccessful. I presume it is possible though? Any help would be much appreciated, Scott [[alternative

...original object (not returning the modified copy of it an overwrite the original by assignment)? Thanks, S?ren setClass("Foo", representation( N = "numeric" ), prototype( N = 10000 ) ) .foo.update <- function(object, ...) { args <- list(...) for (i in slotNames("Foo")[pmatch(names(args), slotNames("Foo"), nomatch=0)]) { slot(object, i) <- args[[i]] # indeed more to do here return(object) } } setReplaceMethod("$", "Foo", function(x, name, value) { x <- .foo.update(x, name=value) x } )...

...e manipulated in qGIS mymcp<-readOGR(dsn=mcp.dir,layer="All mantas MCP land differenc") My spatial points data frame has a number of "Slot"s, including one that contained the original names called Slot "ID". However, I can not access this slot using slot() or slotNames(). > slotNames(mymcp) [1] "data" "polygons" "plotOrder" "bbox" "proj4string" What am I missing here? Is Slot "ID" not a slot? Can I export the ID's with the shapefiles to qGIS? Can I rename the ID's when...

Dear r-help list members, Is there a way to test whether an object is an S4 object? The best that I've been able to come up with is isS4object <- function(object) !(is.null(slotNames(object))) which assumes that an S4 object has at least one slot. I think this is safe, but perhaps I'm missing something. Thanks, John -------------------------------- John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcm...

Dear r-help list members, Is there a way to test whether an object is an S4 object? The best that I've been able to come up with is isS4object <- function(object) !(is.null(slotNames(object))) which assumes that an S4 object has at least one slot. I think this is safe, but perhaps I'm missing something. Thanks, John -------------------------------- John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcm...

...orm some checks on children slots. Say, I want to check if number of slots in a class is equal to "n": setClass("A", representation(a="numeric", n="integer"), prototype=list(a=12, n=1L), validity=function(object){ if(length(slotNames(object))!=object at n+1) paste("Number of slots must be ", object at n) else TRUE }) setClass("B", representation(b="numeric"), contains="A", prototype=list(a=12, b=14, n=2L)) new("B", a=11, b=33) Error in val...

...ject. How can I call parts of that object without using the specific names of the object in the call? example code: library(pcaMethods) myMatrix <- matrix(runif(1e4), ncol=100) ## silly, but sufficient for example myPCA <- pca(myMatrix) ## creates a "pcaRes" S4 class for (i in slotNames(myPCA) ) { summary(myPCA@i) ### I know this doesn't work, but this is the question... what grammar could I use? } ################ I would like to be able to print out the summary for each of the components of the class "pcaRes" without knowing a priori the names of those comp...