[R] adonis (vegan package) and subsetted factors

[Jari Oksanen]

On 10 Apr 2008, at 18:57, tyler wrote:

> On Thu, Apr 10, 2008 at 04:47:44PM +0100, Gavin Simpson wrote:
>>
>> This behaviour arises from the following, using the in-built dune  
>> data:
>>
>>> newdune.env <- subset(dune.env, Management != "NM")
>>> newdune.env$Management
>> [1] BF SF SF SF HF SF HF HF BF BF HF SF SF HF
>> Levels: BF HF NM SF
>>
>> Notice this hasn't dropped the empty level "NM", and this is what is
>> catching out adonis --- it is not checking for empty levels in the
>> grouping factor, as this shows:
>>
>>> newdune <- dune[which(dune.env$Management != "NM"), ]
>>> adonis(newdune ~ Management*A1, data=newdune.env, permutations=100)
>>
>> Call:
>> adonis(formula = newdune ~ Management * A1, data = newdune.env,
>> permutations = 100)
>>
>>                    Df SumsOfSqs  MeanSqs  F.Model     R2 Pr(>F)
>> Management     3.00000   0.57288  0.19096  1.27735 0.2694  <0.01 ***
>>
>> For now, forcibly remove empty factor levels as per your second  
>> example,
>> but I'll take a look at fixing adonis()
>
> Great, thanks!

Howdy folks,

Fine that this was taken care of while my wife and I were seeing  
Fellini's 8 1/2 in our laptop. Actually, this same problem recently  
emerged in varpart and could be lurking elsewhere in vegan. With some  
luck, this fix would have made its way to the latest minor CRAN  
release of vegan we had today. Unfortunately the Earth is designed so  
that you folks over there in Canada are lagging behind, and you were  
still asleep when we had our release here in Europe. It seems that  
CRAN was fast today, and the new version already is available as a  
source and Windows binary in the main CRAN home. With our faster  
release cycles this will be in CRAN rather soon, and it is immediately  
(or from our morning and Canada's late night) in packages at R-Forge.

Best wishes, Jari Oksanen