R help - Aug 2010 - Kruskal Walllis test

Hi all
My data table (g) contains a continues data column (plant.height) and other
columns (columns 8 to 57), 

each with number of levels of different factors.  ANOVA test was done and
the p-values were extracted 

as follos:

a <- function(x) anova(lm(plant.height ~ x))$"Pr(>F)"[1]

r<- apply(g[,8:57],2,a)

If I try to do a Kruskal-Wallis test :

kw <- function(x) kruskal.test(plant.height ~ x)$"p.value"

r.kw <- apply(g[,8:57],2,kw)

I get the following error message:

Error in kruskal.test.default(c(0.16, 0, 0.007, 0.078, 0, 0.08, 0.19,  :

all group levels must be finite

Why do I get this error ? (the values in c() are the plant.height values)

Thanks


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I would suggest to you the following:
1) Run the same thing, but with a loop instead of apply
2) add the to loop a printing that shows you on what cycle of the loop the
function breaks
3) see if that vector has any Inf or NA values (although in general I think
you are using a numeric instead of a factor on the function, which might be
the source of the problem)
4) if you can't figure what is wrong there - use "dput", and put
that vector
on text, and e-mail it back so we could see if we can reproduce the error
and find a reason for it.
5) Report if you found a solution on yourself - so others would benefit from
your experience.

Cheers :)
Tal

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On Tue, Aug 3, 2010 at 2:47 PM, imrib <bisrael@agri.huji.ac.il> wrote:
>
> Hi all
> My data table (g) contains a continues data column (plant.height) and other
> columns (columns 8 to 57),
>
> each with number of levels of different factors.  ANOVA test was done and
> the p-values were extracted
>
> as follos:
>
> a <- function(x) anova(lm(plant.height ~ x))$"Pr(>F)"[1]
>
> r<- apply(g[,8:57],2,a)
>
> If I try to do a Kruskal-Wallis test :
>
> kw <- function(x) kruskal.test(plant.height ~ x)$"p.value"
>
> r.kw <- apply(g[,8:57],2,kw)
>
> I get the following error message:
>
> Error in kruskal.test.default(c(0.16, 0, 0.007, 0.078, 0, 0.08, 0.19,  :
>
> all group levels must be finite
>
> Why do I get this error ? (the values in c() are the plant.height values)
>
> Thanks
>
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/Kruskal-Walllis-test-tp2311712p2311712.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> 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.
>
	[[alternative HTML version deleted]]

The apply function coerces the factor results to a character array
apply(g,2,class) # gives character

The kruskal.test function doesn't take character vector as the group
argument.
kruskal.test(as.character(plant.height) ~ as.character(g[,8])) #doesn't work
kruskal.test(plant.height ~ as.character(g[,8])) #doesn't work
kruskal.test(as.character(plant.height) ~ g[,8]) #works

You'd better change the kw function.
kw <- function(x) kruskal.test(plant.height ~
as.factor(x))$"p.value"

-----
A R learner.
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On Aug 3, 2010, at 1:47 PM, imrib wrote:
> 
> Hi all
> My data table (g) contains a continues data column (plant.height) and other
> columns (columns 8 to 57), 
> 
> each with number of levels of different factors.  ANOVA test was done and
> the p-values were extracted 
> 
> as follos:
> 
> a <- function(x) anova(lm(plant.height ~ x))$"Pr(>F)"[1]
> 
> r<- apply(g[,8:57],2,a)
This looks like an invitation to disaster. apply() will coerce g[,8:57] to a
matrix, losing all factor definitions. As it happens, lm() will survive this,
because
> lm(0:1~c("a","b"))
Call:
lm(formula = 0:1 ~ c("a", "b"))

Coefficients:
 (Intercept)  c("a", "b")b  
           0             1  

Warning message:
In model.matrix.default(mt, mf, contrasts) :
  variable 'c("a", "b")' converted to a factor

But kruskal.test dies on the similar construction, essentially because
> is.finite("a")
[1] FALSE
................

Try it with lapply(g[,8:57], kw) instead.

-pd

> 
> If I try to do a Kruskal-Wallis test :
> 
> kw <- function(x) kruskal.test(plant.height ~ x)$"p.value"
> 
> r.kw <- apply(g[,8:57],2,kw)
> 
> I get the following error message:
> 
> Error in kruskal.test.default(c(0.16, 0, 0.007, 0.078, 0, 0.08, 0.19,  :
> 
> all group levels must be finite
> 
> Why do I get this error ? (the values in c() are the plant.height values)
> 
> Thanks
> 
> 
> -- 
> View this message in context:
http://r.789695.n4.nabble.com/Kruskal-Walllis-test-tp2311712p2311712.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> ______________________________________________
> R-help at 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.
-- 
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com