Janh,
Janh Anni skrev 2013-06-01 19:47:
Hello All,
Thanks a lot for the helpful suggestions. I wonder how ties are handled
for the rank sum test by wilcox_test and wilcox.exact? For instance,
Ties handling was mainly a problem back in the day when recursion
formulas were used for the computation of exact p-values. (When no ties
are present, the form of the exact null distribution of the Wilcoxon
rank-sum statistic depends only on the total number of observations in
the two groups.)
other software such as Minitab correct for ties by adjusting the
variance of the test statistic, and actually provide the p values before
and after adjustment for ties.
Adjusting the variance only matters when approximating the exact
distribution with its asymptotic Gaussian distribution. And only when
at least one tie is shared between the two groups. And yes, the
standardized statistic in 'coin' accounts for ties. If ties are
present, why would you want to know the unadjusted p-value?
IIf neither wilcox_test nor wilcox.exact
expressly corrects for ties in the Wilcoxon rank sum test, then perhaps
one should just use the conventional wilcox.test which is the simplest
> of them all? Thanks again
If this was true, the 'wilcox.exact' function would be completely
pointless since 'wilcox.test' just falls back on the asymptotic
approximation when ties are present.
Software like 'StatXact', 'exactRankTests', and 'coin' use algorithms
that compute the exact p-value for any ties configuration. Take a look
at Torsten Hothorn's "On Exact Rank Tests in R" article from the very
first issue of R News http://www.r-project.org/doc/Rnews/Rnews_2001-1.pdf.
Henric
Janh
On Sat, Jun 1, 2013 at 8:41 AM, Henric Winell <nilsson.hen...@gmail.com
<mailto:nilsson.hen...@gmail.com>> wrote:
Janh,
Janh Anni skrev 2013-06-01 04:27:
Hello peter,
Thanks for the comment. wilcox.exact is simpler as you pointed
out but the
fact that it is no longer being developed is somewhat concerning.
Admittedly, 'coin' is being actively developed and has a lot more
bells and whistles. But for something as simple as this, that
wouldn't bother me at all. In any case, the 'exactRankTests'
package still gets bug fixes and the algorithm used in the Wilcoxon
case is exactly the same for both packages.
However, if you want to stay with 'coin' you can just wrap up Greg's
proposal in a function:
wilcox_test.default <- function(x, y, ...) {
data <-
data.frame(values = c(x, y),
group = rep(c("x", "y"), c(length(x), length(y))))
wilcox_test(values ~ group, data = data, ...)
}
Assuming that both 'coin' and 'exactRankTests are loaded, we can now
check that it works:
> set.seed(123)
> x <- rpois(10, 3)
> y <- rpois(11, 3.1)
>
> wilcox_test(x, y, alternative = "less", distribution = "exact")
Exact Wilcoxon-Mann-Whitney Test
data: values by group (x, y)
Z = -0.0715, p-value = 0.4844
alternative hypothesis: true mu is less than 0
> wilcox.exact(x, y, alternative = "less")
Exact Wilcoxon rank sum test
data: x and y
W = 54, p-value = 0.4844
alternative hypothesis: true mu is less than 0
HTH,
Henric
Regards
Janh
On Fri, May 31, 2013 at 6:50 PM, Peter Ehlers
<ehl...@ucalgary.ca <mailto:ehl...@ucalgary.ca>> wrote:
On 2013-05-30 20:20, Janh Anni wrote:
Hello Greg,
Thank you so much for your kind assistance. It looks
like there's no way
around using the formula format. I longed in vain for a
simpler script
more like the wilcox.test format. Thanks again.
Janh
I don't see why the formula syntax would be a problem, but
to avoid it
you could use exactRankTests::wilcox.exact() which, I
believe, was
written by the same author. It uses the same syntax as
wilcox.test().
Note, though, that the package is no longer
being developed.
Peter Ehlers
On Thu, May 30, 2013 at 6:21 PM, Greg Snow
<538...@gmail.com <mailto:538...@gmail.com>> wrote:
Ok, it looks like the function mainly works through
the formula syntax.
It still would have been nice to have a
reproducible example of what
your
data may look like, but I can show an example with
simulated x and y:
x <- rpois(10, 3)
y <- rpois(11, 3.1)
mydf <- data.frame( vals = c(x,y),
+ group=rep( c('x','y'), c( length(x), length(y) ) ) )
wilcox_test( vals ~ group, data=mydf )
Asymptotic Wilcoxon-Mann-Whitney Test
data: vals by group (x, y)
Z = -1.3718, p-value = 0.1701
alternative hypothesis: true mu is not equal to 0
Does that help? (maybe I am the heedlessness
theorist after all)
On Thu, May 30, 2013 at 4:14 PM, Janh Anni
<annij...@gmail.com <mailto:annij...@gmail.com>> wrote:
I thought (hoped) wilcox_test(x,y) would do it
but it doesn't and the
package maintainer says the data have to be
rearranged but does not
specify
how. Thanks
Janh
On Thu, May 30, 2013 at 6:05 PM, Greg Snow
<538...@gmail.com <mailto:538...@gmail.com>> wrote:
What have you tried so far? Have you read
the help page? have you run
the examples on that page?
I would expect that it is something as simple as
library(coin)
wilcox_test(x,y)
or
wilcox_test( y ~ group )
But you should trust the help page more than
the expectations of
someone
who has not read it recently (see fortune(14)).
If that does not answer your question then
give us more detail on what
you tried, what you expected the results to
be, what the results
actually
were, and how they differed. Without that
information we have to
resort to
mind reading and the current implementation
of the esp package is still
very pre-alpha, it suggests that the answer
to your question is:
esp()
[1] "selflessly vigilantly pigeon theorist
heedlessness"
Which is either much to profound for the
likes of me to understand or
is
complete gibberish (which is only slightly
less helpful than an overly
general question without a reproducible
example).
On Thu, May 30, 2013 at 2:07 PM, Janh Anni
<annij...@gmail.com
<mailto:annij...@gmail.com>> wrote:
Dear All,
I have two simple data samples (no
groups or factors, etc.) and would
just
like to compute the two-sample Wilcoxon
Rank Sum test using the
wilcox_test
function contained in the coin package,
which is reportedly better
than
the
regular wilcox.test function because it
performs some adjustment for
ties.
Would anyone know how to craft a script
to perform this task? Much
appreciated.
Janh
[[alternative HTML version
deleted]]
________________________________**________________
R-help@r-project.org
<mailto:R-help@r-project.org> mailing list
https://stat.ethz.ch/mailman/*__*listinfo/r-help
<https://stat.ethz.ch/mailman/**listinfo/r-help><https://stat__ethz.ch/mailman/listinfo/r-__help
<https://stat.ethz.ch/mailman/listinfo/r-help>>
PLEASE do read the posting guide
http://www.R-project.org/**__posting-guide.html
<http://www.R-project.org/**posting-guide.html><http://www.__R-project.org/posting-guide.__html
<http://www.R-project.org/posting-guide.html>>
and provide commented, minimal,
self-contained, reproducible code.
--
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com <mailto:538...@gmail.com>
--
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com <mailto:538...@gmail.com>
[[alternative HTML version deleted]]
________________________________**________________
R-help@r-project.org <mailto:R-help@r-project.org>
mailing list
https://stat.ethz.ch/mailman/*__*listinfo/r-help
<https://stat.ethz.ch/mailman/**listinfo/r-help><https://stat__ethz.ch/mailman/listinfo/r-__help
<https://stat.ethz.ch/mailman/listinfo/r-help>>
PLEASE do read the posting guide http://www.R-project.org/**
posting-guide.html
<http://www.R-project.org/__posting-guide.html
<http://www.R-project.org/posting-guide.html>>
and provide commented, minimal, self-contained,
reproducible code.
[[alternative HTML version deleted]]
________________________________________________
R-help@r-project.org <mailto:R-help@r-project.org> mailing list
https://stat.ethz.ch/mailman/__listinfo/r-help
<https://stat.ethz.ch/mailman/listinfo/r-help>
PLEASE do read the posting guide
http://www.R-project.org/__posting-guide.html
<http://www.R-project.org/posting-guide.html>
and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
