[R] multiple paired t-tests without loops

[Matthew Finkbeiner]

I am new to R and I suspect my problem is easily solved, but I haven't 
been able to figure it out without using loops.  I am trying to 
implement Blair & Karniski's (1993) permutation test.  I've included a 
sample data frame below.  This data frame represents the conditional 
means (C1, C2) for 3 subjects in 2 consecutive samples of a continuous 
data set (e.g. ERP waveform).  Each sample includes all possible 
permuations of the subject means (2^N), which is 8 in this case.

The problem: I need to run a paired t-test on each SampleXPermutation 
set and save the maximum t-value obtained for each sample.  The real 
data set has 16 subjects (216 permutations) and 500 samples, which leads 
to more than 32 million t-tests.  I have a loop version of the program 
working, but it would take a few weeks to complete the job and I was 
hoping that someone could tell me how to do it faster?

thank you kindly,

Matthew Finkbeiner

--------------------------------

"Sample"    "C1"    "C2"    "PermN"
1    5    8    perm1
1    4    3    perm1
1    6    4    perm1
2    2    6    perm1
2    3    1    perm1
2    7    4    perm1
1    8    5    perm2
1    3    4    perm2
1    6    4    perm2
2    6    2    perm2
2    1    3    perm2
2    7    4    perm2
1    5    8    perm3
1    3    4    perm3
1    6    4    perm3
2    2    6    perm3
2    1    3    perm3
2    7    4    perm3
1    8    5    perm4
1    4    3    perm4
1    4    6    perm4
2    6    2    perm4
2    3    1    perm4
2    4    7    perm4
1    5    8    perm5
1    4    3    perm5
1    4    6    perm5
2    2    6    perm5
2    3    1    perm5
2    4    7    perm5
1    8    5    perm6
1    3    4    perm6
1    4    6    perm6
2    6    2    perm6
2    1    3    perm6
2    4    7    perm6
1    5    8    perm7
1    3    4    perm7
1    4    6    perm7
2    2    6    perm7
2    1    3    perm7
2    4    7    perm7
1    8    5    perm8
1    4    3    perm8
1    6    4    perm8
2    6    2    perm8
2    3    1    perm8
2    7    4    perm8






-- 
Dr. Matthew Finkbeiner
Senior Lecturer & ARC Australian Research Fellow
Macquarie Centre for Cognitive Science (MACCS)
Macquarie University, Sydney, NSW 2109

Phone: +61 2 9850-6718
Fax:   +61 2 9850-6059
Homepage: http://www.maccs.mq.edu.au/~mfinkbei
Lab Homepage: http://www.maccs.mq.edu.au/laboratories/action/