R help - May 2012 - bigmemory

To answer your first question about read.big.matrix(), we don't know what
your acc3.dat file is, but it doesn't appear to have been detected as a
standard file (like a CSV file) or -- perhaps -- doesn't even exist (or
doesn't exist in your current directory)?

Next:
> In addition, I am planning to do a multiple imputation with MICE package
> using the data read by bigmemory package.
> So usually, the multiple imputation code is like this:
 > imp=mice(data.frame,m=50,seed=1234,print=F)
> the data.frame is required. How can I change the big.matrix class
> generated by bigmemory package to a data.frame?
Please read the help files for bigmemory -- only matrix-like objects are
supported.  However, the more serious problem is that you can't expect to
run just any R function on a big.matrix (or on an ff object, if you check
out ff for some nice features).  In particular, for large data sets you
would likely use up all of RAM (other reasons are more subtle and
important, but out of place in this reply).

Jay

-- 
John W. Emerson (Jay)
Associate Professor of Statistics
Department of Statistics
Yale University
http://www.stat.yale.edu/~jay

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Hi Jay,

I have a question about your reply.

You mentioned that "the more serious problem is that you can't expect
to run just any R function on a big.matrix (or on an ff object, if you check out
ff for some nice features).  "

I am confused why the packages could not communicate with each other. I
understand that maybe for some programming or statistical reasons, one package
need its own "class" so that specific algorithm can be implemented.
However, R as a statistical programming environment, one of its advantages is
the abundance of the packages under R structure. If different packages generate
different kinds of object and can not be recognized and used for further
analysis by other packages, then each package would appears to be similar with
the normal independent software, e.g., SAS, MATLAB... then this could reduce the
whole R ability for handling complicated analysis situation.

This is just a general thought.

Thank you very much.




ya

From: Jay Emerson
Date: 2012-05-11 14:44
To: ya; r help
Subject: RE: bigmemory


To answer your first question about read.big.matrix(), we don't know what
your acc3.dat file is, but it doesn't appear to have been detected as a
standard file (like a CSV file) or -- perhaps -- doesn't even exist (or
doesn't exist in your current directory)?

Next:
> In addition, I am planning to do a multiple imputation with MICE package
> using the data read by bigmemory package.
> So usually, the multiple imputation code is like this:
 > imp=mice(data.frame,m=50,seed=1234,print=F)
> the data.frame is required. How can I change the big.matrix class
> generated by bigmemory package to a data.frame?
Please read the help files for bigmemory -- only matrix-like objects are
supported.  However, the more serious problem is that you can't expect to
run just any R function on a big.matrix (or on an ff object, if you check out ff
for some nice features).  In particular, for large data sets you would likely
use up all of RAM (other reasons are more subtle and important, but out of place
in this reply).

Jay

-- 
John W. Emerson (Jay)
Associate Professor of Statistics
Department of Statistics
Yale University
http://www.stat.yale.edu/~jay
	[[alternative HTML version deleted]]