[R] Size of a refClass instance

Martin Morgan mtmorgan at fhcrc.org
Thu May 2 22:57:31 CEST 2013

On 05/01/2013 11:20 AM, David Kulp wrote:
> I'm using refClass for a complex multi-directional tree structure with
> possibly 100,000s of nodes.  The refClass design is very impressive and I'd
> love to use it, but I've found that the size of refClass instances are very
> large and creation time is slow.  For example, below is a RefClass and normal
> S4 class.  The RefClass requires about 4KB per instance vs 500B for the S4
> class -- based on adding the Ncells and Vcells of used memory reported by
> gc().  And instantiation is more than twice as slow for a RefClass.  (R
> 2.14.2)
> Anyone have thoughts on this and whether there's any hope for improving
> resources on either front?

Hi David -- not necessarily helpful but creating a few large objects is always 
better than creating many small in R, so perhaps re-conceptualize your data 
structure? As a rough analogy, instead of constructing a graph as a large number 
of 'Node' instances each pointing to one another, a graph could be represented 
as a data.frame containing columns of 'from' and 'to' indexes (neighbour-edge 
list, a few large objects) or as an adjacency matrix. One would also implement 
creation and update of the few large objects in an R-friendly (vectorized) way.

Perhaps there are existing packages that already model the data you're 
interested in? If your multi-directional tree can be represented as a graph, 
then perhaps


including facilities in the Boost graph library (RBGL, on the Bioconductor web 
site, too) or the igraph package can be put to use.


> I wonder what others are doing.  I've been thinking about lightweight
> alternative implementations, but nothing particularly elegant has come to
> mind, yet!
> Thanks!
> simple <- setRefClass('simple', fields = list(a = "character", b="numeric")
> ) gc() system.time(simple.list <- lapply(1:100000, function(i) {
> simple$new(a='foo',b=i) })) gc()
> setClass('simple2', representation(a="character",b="numeric"))
> setMethod("initialize", "simple2", function(.Object, a, b) { .Object at a <- a
> .Object at b <- b .Object })
> gc() system.time(simple2.list <- lapply(1:100000, function(i) {
> new('simple2',a='foo',b=i) })) gc()
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