[R-sig-eco] vegan: goodness() and pRDA

[Christoph Eberhard Freiherr von Redwitz]

Hi all!
I am using rda() in vegan and goodness() as a diagnostic tool. I want to know how good the species fit to the first two ordination axes.
But I got problems combining partial RDA and goodness(). The species sum of CA and CCA don't add up to 1 (as it does in RDA without Condition term). Furthermore, I get warnings when only one axis is left over in the result of goodness.
Here an example:


#########----------------------------------------------#############
data(dune)
data(dune.env)

mod1 <- rda(dune~A1 + Moisture + Management, data=dune.env)
mod2  <- rda(dune~ Manure + Condition(A1 + Moisture + Management), data=dune.env)
mod3 <- rda(dune~A1 + Condition(Manure + Moisture + Management), data=dune.env)

goodness(mod1, mod= "CA ",sum=T) + goodness(mod1, mod= "CCA ",sum=T)#result as expected
goodness(mod2, mod= "CA ",sum=T) + goodness(mod2, mod= "CCA ",sum=T)#only 4 RDA axes left over, they don't end up with 1

#here comes the warning:
goodness(mod3,mod= "CA ",sum=T)#works
goodness(mod3,mod= "CCA",sum=T) #only 1 RDA axis left. Warning messages. The "sum" option seems to be affected.
#########----------------------------------------------#############

Two questions:
Is the warning because of wrong usage of the method? Can I use goodness with partial RDA?
1 - goodness(mod3,mod= "CA ",sum=T) should do it in this case?

I hope the mail is clear and not an old story.

Greetings!
Christoph


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