R help - Oct 2014 - kruskal test p value way too low.

Hello,

I'm trying to run kruskal test on some data but the p values seemed way too
low.  So I tried it on some similar data and still got p-value 1.611e-09. 
I'm sure it is a simple mistake but I can't figure it out.

Below is my data and code.  Could it be because there are some miss data /
NAs in the data set??  If so, could some one point me towards a solution??

Thank you for your time.
David

mydata <-read.csv("http://doylesdartden.com/R/test.csv",
sep=",")
kruskal.test(mydata, AMMONIA~Well)

        Kruskal-Wallis rank sum test

data:  mydata
Kruskal-Wallis chi-squared = 36.3952, df = 1, p-value = 1.611e-09

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On 26/10/14 16:40, David Doyle wrote:
> Hello,
>
> I'm trying to run kruskal test on some data but the p values seemed way
too
> low.  So I tried it on some similar data and still got p-value >
1.611e-09.  I'm sure it is a simple mistake but I can't figure it out.
>
> Below is my data and code.  Could it be because there are some miss data /
> NAs in the data set??  If so, could some one point me towards a solution??
>
> Thank you for your time.
> David
>
> mydata <-read.csv("http://doylesdartden.com/R/test.csv",
sep=",")
> kruskal.test(mydata, AMMONIA~Well)
>
>          Kruskal-Wallis rank sum test
>
> data:  mydata
> Kruskal-Wallis chi-squared = 36.3952, df = 1, p-value = 1.611e-09
Thank you for providing a clear question and an easily reproducible example.

The problem is your syntax for the call to the kruskal.test() function.

It should be:

     kruskal.test(AMMONIA ~ Well, data=mydata)

This gives a p-value of 1 (which agrees with wilcox.test); t.test() 
gives a p-value of 0.7958) so harmony is restored to the universe.

IMHO there is a bit of a design flaw in kruskal.test(); it should have 
thrown an error, given your syntax.  The wilcox.test() function *does* 
throw an error.

cheers,

Rolf Turner

-- 
Rolf Turner
Technical Editor ANZJS