Ivan Adzhubey
2008-Mar-12 21:10 UTC
[R] Problem with approximate null distribution (package: coin)
Hi, I am trying to make use of "approximate" option to obtain null distribution through Monte-Carlo resampling, as described in coin library documentation. Unfortunately, this does not play well with my data -- permutation process swallows astonishingly large amounts of RAM (4-5Gb) and runs far too long (30 min for B=10). Apparently, this is caused by the size of my dataset (see example below) but I was under impression that permutation algorithm just draws random contingency tables from the fixed conditional marginals, in which case the amount of memory required should not depend on the dataset size very much, as well as the execution time should only depend on B. Obviously, I was wrong about both assumptions. Is there any reasonable way to work around these limitations in case of a large dataset? It's not that large in fact, so I am a bit surprised the efficiency of resampling is so poor. Below is the dataset example, what I am trying to do is perform cmh_test() on a 4x2x3 table.> adata, , Content = low Response Time Yes No 0 384 597259 1 585 888039 2 621 896102 3 1466 1606456 , , Content = medium Response Time Yes No 0 101 99525 1 160 191698 2 173 146814 3 469 485012 , , Content = high Response Time Yes No 0 119 175938 1 167 163881 2 77 131063 3 522 548924 --Ivan The information transmitted in this electronic communica...{{dropped:10}}