Re: [R] memory problem for R

Spencer Graves Fri, 30 Jan 2004 12:43:30 -0800

Was your 10% sample contiguous or randomly selected from the entire file? If contiguous, you might get something from, say, processing the file in 100 contiguous blocks, computing something like the mean of each 1% block (or summarizing in some other way within blocks), then combining the summaries and do regression on block summaries.

If it was an honest random sample (e.g., selecting approximately 10% from each 10%), then the block averaging won't work: You have an inherent singularity in the structure of the data that will likely not permit you to estimate everything you want to estimate. You need to understand that singularity / lack of estimability and decide what to do about it.

In either case, "lm(..., singular.ok=T)" will at least give you an answer even when the model is not fully estimable.

hope this helps. spencer graves

Yun-Fang Juan wrote:

Pleaase see the comments below.
Here is the exact error I got ---------------------- Read 73 items Error: cannot allocate vector of size 1953 Kb Execution halted ----------------------- I am running R on Freebsd 4.3 with double CPU and 2 GB memory Is that sufficient?
Clearly not.  What is the structure of your `attributes'?  As Andy Liaw
said, the design matrix may be bigger than that if there are factors
involved.  (And you need several copies of the design matrix.)
I would try a 10% sample of the rows to get a measure of what will fit into your memory. I have never seen a regression problem for which 600k cases were needed, and would be interested to know the context. (It is hard to imagine that the cases are from a single homogeneous population and that a linear model fits so well that the random error is not dominated by systematic error.)
I tried 10% sample and it turned out the matrix became singular after I did
that.
Ther reason is some of the attributes only have zero values most of the
time.
The data i am using is web log data and after some transformation, they are
all numeric.
Can we specify some parameters in read.table so that the program will treat
all the vars as numeric
(with this context, hopefully that will reduce the memory consumption)  ?
thanks a lot,

Yun-Fang
Yun-Fang
----- Original Message -----
From: "Yun-Fang Juan" <[EMAIL PROTECTED]>
To: <[EMAIL PROTECTED]>
Sent: Thursday, January 29, 2004 7:03 PM
Subject: [R] memory problem for R
Hi, I try to use lm to fit a linear model with 600k rows and 70
attributes.
But I can't even load the data into the R environment.
The error message says the vector memory is used up.
Is there anyone having experience with large datasets in R? (I bet)

Please advise.

thanks,

Yun-Fang

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Re: [R] memory problem for R

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