From simon.urbanek at r-project.org  Tue Jan  3 22:59:24 2012
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Tue, 3 Jan 2012 16:59:24 -0500
Subject: [Rd] returning information from functions via attributes rather
	than return list
In-Reply-To: <CAErODj8GiAnVbirM5JtdFAOBqPrqa+XcEagy5RYRhofdqrQ+QA@mail.gmail.com>
References: <CAErODj8GiAnVbirM5JtdFAOBqPrqa+XcEagy5RYRhofdqrQ+QA@mail.gmail.com>
Message-ID: <B12E72A9-7A9F-467E-822C-737561B3B06D@r-project.org>

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
> 
> 



[Rd] returning information from functions via attributes rather than return list
Simon Urbanek