

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
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