Re: [Rd] returning information from functions via attributes rather than return list

From: Simon Urbanek <simon.urbanek_at_r-project.org>
Date: Tue, 03 Jan 2012 16:59:24 -0500

Paul,

On Jan 3, 2012, at 3:08 PM, Paul Johnson wrote:

> I would like to ask for advice from R experts about the benefits or
> dangers of using attr to return information with an object that is
> returned from a function. I have a feeling as though I have cheated by
> using attributes, and wonder if I've done something fishy.
>
> Maybe I mean to ask, where is the dividing line between attributes and
> instance variables? The separation is not clear in my mind anymore.
>
> Background: I paste below a function that takes in a regression object
> and make changes to the data and/or call and then run a
> revised regression. In my earlier effort, I was building a return
> list, including the new fitted regression object plus some
> variables that have information about the changes that a were made.
>
> That creates some inconvenience, however. When the regression is in a
> list object, then methods for lm objects don't apply to that result
> object. The return is not an lm anymore.

Why don't you just subclass it? That's the "normal" way of doing things - you simply add additional entries for your subclass (e.g. m$myItem1, m$myItem2, ...), prepend your new subclass name and you're done. You can still dispatch on your subclass before the superclass while superclass methods just work as well..

Cheers,
Simon

> I either need to write
> custom methods for every function or remember to extract the object
> from the list before sending to the generic function.
>
> I *guessed* it would work to write the new information as object
> attributes, and it seems to work. There is a generic function
> "meanCenter" and a method "meanCenter.default". At the end of
> meanCenter.default, here's my use (or abuse) of attributes.
>
> res <- eval(mc)
> class(res) <- c("mcreg", class(model))
> attr(res, "centeredVars") <- nc
> attr(res, "centerCall") <- match.call()
> res
>
> I wrote print and summary methods, but other methods that work for lm
> objects like plot will also work for these new ones.
>
>
>
> meanCenter <- function(model, centerOnlyInteractors=TRUE,
> centerDV=FALSE, standardize=FALSE, centerContrasts = F){
> UseMethod("meanCenter")
> }
>
> meanCenter.default <- function(model, centerOnlyInteractors=TRUE,
> centerDV=FALSE, standardize=FALSE, centerContrasts = F){
>
> std <- function(x) {
> if( !is.numeric(x) ){
> stop("center.lm tried to center a factor variable. No Can Do!")
> } else {
> scale(x, center = TRUE, scale = standardize)
> }
> }
>
> rdf <- get_all_vars(formula(model), model$model) #raw data frame
> t <- terms(model)
> tl <- attr(t, "term.labels")
> tmdc <- attr(t, "dataClasses") ##term model data classes
>
> isNumeric <- names(tmdc)[ which(tmdc %in% c("numeric"))]
> isFac <- names(tmdc)[ which(tmdc %in% c("factor"))]
> if (tmdc[1] != "numeric") stop("Sorry, DV not a single numeric column")
>
> ##Build "nc", a vector of variable names that "need centering"
> ##
> if (!centerDV) {
> if (centerOnlyInteractors == FALSE){
> nc <- isNumeric[-1] #-1 excludes response
> unique(nc)
> }else{
> interactTerms <- tl[grep(":", tl)]
> nc <- unique(unlist(strsplit( interactTerms, ":")))
> nc <- nc[which(nc %in% isNumeric)]
> }
> }else{
> if (centerOnlyInteractors == FALSE){
> nc <- isNumeric
> }else{
> interactTerms <- tl[grep(":", tl)]
> nc <- unique(unlist(strsplit( interactTerms, ":")))
> nc <- nc[which(nc %in% isNumeric)]
> nc <- c( names(tmdc)[1] , nc)
> }
> }
>
>
> mc <- model$call
> # run same model call, replacing non centered data with centered data.
> ## if no need to center factor contrasts:
> if (!centerContrasts)
> {
> stddat <- rdf
> for (i in nc) stddat[ , i] <- std( stddat[, i])
> mc$data <- quote(stddat)
> }else{
> ##dm: design matrix, only includes intercept and predictors
> dm <- model.matrix(model, data=rdf, contrasts.arg =
> model$contrasts, xlev = model$xlevels)
> ##contrastIdx: indexes of contrast variables in dm
> contrastIdx <- which(attr(dm, "assign")== match(isFac, tl))
> contrastVars <- colnames(dm)[contrastIdx]
> nc <- c(nc, contrastVars)
>
> dm <- as.data.frame(dm)
>
> hasIntercept <- attr(t, "intercept")
> if (hasIntercept) dm <- dm[ , -1] # removes intercept, column 1
>
> dv <- rdf[ ,names(tmdc)[1]] #tmdc[1] is response variable name
> dm <- cbind(dv, dm)
> colnames(dm)[1] <- names(tmdc)[1] #put colname for dv
>
> dmnames <- colnames(dm)
> hasColon <- dmnames[grep(":", dmnames)]
> dm <- dm[ , -match(hasColon, dmnames)] ##remove vars with colons
> (lm will recreate)
>
> ##Now, standardise the variables that need standardizing
> for (i in nc) dm[ , i] <- std( dm[, i])
>
>
> fmla <- formula(paste(dmnames[1], " ~ ", paste(dmnames[-1],
> collapse=" + ")))
> cat("This fitted model will use those centered variables\n")
> cat("Model-constructed interactions such as \"x1:x3\" are built
> from centered variables\n")
> mc$formula <- formula(fmla)
> mc$data <- quote(dm)
> }
>
> cat("These variables", nc, "Are centered in the design matrix \n")
>
> res <- eval(mc)
> class(res) <- c("mcreg", class(model))
> attr(res, "centeredVars") <- nc
> attr(res, "centerCall") <- match.call()
> res
> }
>
> summary.mcreg <- function(object, ...){
> nc <- attr(object, "centeredVars")
> cat("The centered variables were: \n")
> print(nc)
> cat("Even though the variables here have the same names as their
> non-centered counterparts, I assure you these are centered.\n")
> mc <- attr(object, "centerCall")
> cat("These results were produced from: \n")
> print(mc)
> NextMethod(generic = "summary", object = object, ...)
> }
>
>
> print.mcreg <- function(x, ...){
> nc <- attr(x, "centeredVars")
> cat("The centered variables were: \n")
> print(nc)
> cat("Even though the variables here have the same names as their
> non-centered counterparts, I assure you these are centered.\n")
> mc <- attr(x, "centerCall")
> cat("These results were produced from: \n")
> print(mc)
> NextMethod(generic = "print", object = x, ...)
> }
>
>
> --
> Paul E. Johnson
> Professor, Political Science
> 1541 Lilac Lane, Room 504
> University of Kansas
>
> ______________________________________________
> R-devel_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>



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