On Fri, 23 Apr 2010, Greg Snow wrote:
The perm.test function in exactRankTests makes reference to the StatXact
manual, so presumably that would have the exact details. The details
section of the help file refers to converting real values to integers,
so I expect that it is not doing what many of us think of as a
permutation test, and I would not think that it is using t-statistics.
Well, it is similar to that and even more similar to the Wilcoxon
statistic. But more importantly, perm.test() is superseded by
independence_test() in package "coin" (to which the message at startup of
"exactRankTests" points you), at least for two-sample tests.
The "coin" package is also much better documented, see in particular
vignette("LegoCondInf", package = "coin")
which corresponds to the paper published in The American Statistician, see
citation("coin")
R is powerful enough that a permutation test can be run in just a few
lines of R code without needing a specialized function. And when you do
it that way, you know exactly what is being done.
True, but in some situations there are more efficient sampling algorithms
available, some of which are provided in "coin".
Best,
Z
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
From: Xiang Gao [mailto:xianggao2...@gmail.com]
Sent: Friday, April 23, 2010 8:52 AM
To: Greg Snow; djmu...@gmail.com
Cc: r-help@r-project.org
Subject: Re: [R] What is the test statistics in perm.test
Thanks for all your reply. I am a biologist and only start to use R recently.
Yes, It is my fault. I assume that perm.test is a very popular method. Thanks
for Dennis to point out that it is in exactRankTests package. I did not realize
that there are so many R package. I guess I did not ask the right question and
neither in the right way.
Based on my limited knowledge on statistics, it seems like use t-statistics to
test the permutation. I am just not sure.
Xiang
exactRankTests
On Fri, Apr 23, 2010 at 9:13 AM, Greg Snow
<greg.s...@imail.org<mailto:greg.s...@imail.org>> wrote:
There is no perm.test function in base R, is this from a package? Which
package? What does the documentation for that function/package say?
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org<mailto:greg.s...@imail.org>
801.408.8111
-----Original Message-----
From: r-help-boun...@r-project.org<mailto:r-help-boun...@r-project.org>
[mailto:r-help-boun...@r-<mailto:r-help-boun...@r->
project.org<http://project.org>] On Behalf Of Xiang Gao
Sent: Thursday, April 22, 2010 1:43 PM
To: r-help@r-project.org<mailto:r-help@r-project.org>
Subject: [R] What is the test statistics in perm.test
Hi,
The permutation test for two samples in R is function perm.test(). I
could
not figure out what is the statistics it estimate and how many
permutation
it did in default?
Thanks,
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--
Xiang Gao, Ph.D.
Department of Biology
University of North Texas
[[alternative HTML version deleted]]
______________________________________________
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and provide commented, minimal, self-contained, reproducible code.
______________________________________________
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