From rdpeng at gmail.com  Sat Jun 30 01:44:28 2007
From: rdpeng at gmail.com (Roger Peng)
Date: Fri, 29 Jun 2007 19:44:28 -0400
Subject: [Rd] saving objects with embedded environments
In-Reply-To: <EEBC169715EB8C438D3C9283AF0F201C17C830@MSGBOSCLM2WIN.DMN1.FMR.COM>
References: <EEBC169715EB8C438D3C9283AF0F201C17C830@MSGBOSCLM2WIN.DMN1.FMR.COM>
Message-ID: <66f3bd910706291644s6db3b3a9ncd1bd075ceec3553@mail.gmail.com>

I believe this is intentional.  See ?serialize.  When lm() is called
in a function, the environment is saved in case the resulting fitted
model object needs to be updated, for example, with update().

if you don't want the linear model object, you might try just saving
the relevant objects to a separate list rather than try to delete
everything that is irrelevant from the 'lm' object.

-roger

On 6/28/07, McGehee, Robert <Robert.McGehee at geodecapital.com> wrote:
> Hello,
> I have been running linear regressions on large data sets. As 'lm' saves
> a great deal of extraneous (for me) data including the residuals,
> fitted.values, model frame, etc., I generally set these to NULL within
> the object before saving off the model to a file.
>
> In the below example, however, I have found that depending on whether or
> not I run 'lm' within another function or not, the entire function
> environment is saved off with the file. So, even while object.size and
> all.equal report that both 'lm's are equal and of small size, one saves
> as a 24MB file and the other as 646 bytes. These seems to be because in
> the first example the function environment is saved in attr(x1$terms,
> ".Environment") and takes up all 24MB of space.
>
> Anyway, I think this is a bug, or if nothing else very undesirable (that
> an object reported to be 0.5kb takes up 24MB). There also seems to be
> some inconsistency on how environments are saved depending on if it is
> the global environment or not, though I'm not familiar enough with
> environments to know if this was intentional. Comments are appreciated.
>
> Thanks,
> Robert
>
> ##################################################################
> testEq <- function(B) {
>     x <- lm(y ~ x1+x2+x3, data=B, model=FALSE)
>     x$residuals <- x$effects <- x$fitted.values <- x$qr$qr <- NULL
>     x
> }
>
> N <- 900000
> B <- data.frame(y=rnorm(N)+1:N, x1=rnorm(N)+1:N, x2=rnorm(N)+1:N,
> x3=rnorm(N)+1:N)
> x1 <- testEq(B)
> x2 <- lm(y ~ x1+x2+x3, data=B, model=FALSE)
> x2$residuals <- x2$effects <- x2$fitted.values <- x2$qr$qr <- NULL
>
> all.equal(x1, x2) ## TRUE
> object.size(x1)  ## 5112
> object.size(x2)  ## 5112
> save(x1, file="x1.RData")
> save(x2, file="x2.RData")
> file.info("x1.RData")$size ## 24063852 bytes
> file.info("x2.RData")$size ## 646 bytes
>
> > R.version
>                _
> platform       i686-pc-linux-gnu
> arch           i686
> os             linux-gnu
> system         i686, linux-gnu
> status
> major          2
> minor          5.0
> year           2007
> month          04
> day            23
> svn rev        41293
> language       R
> version.string R version 2.5.0 (2007-04-23)
>
>
> Robert McGehee, CFA
> Quantitative Analyst
> Geode Capital Management, LLC
> One Post Office Square, 28th Floor | Boston, MA | 02109
> Tel: 617/392-8396    Fax:617/476-6389
> mailto:robert.mcgehee at geodecapital.com
>
>
>
> This e-mail, and any attachments hereto, are intended for us...{{dropped}}
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>


-- 
Roger D. Peng  |  http://www.biostat.jhsph.edu/~rpeng/



[Rd] saving objects with embedded environments
Roger Peng