This seems to be a bug in vegan. In fact, there are both bugs and bad design
decisions.
I have pushed a pull request to https://github.com/vegandevs/vegan which fixes
the issues in this message plus a couple of other quirks. I'll test that fix a
bit, and if everything looks OK, it will be merged and included in the next
vegan release.
Thanks for reporting this.
Best wishes, Jari Oksanen
From: R-sig-ecology r-sig-ecology-boun...@r-project.org on behalf of
Christoph Eberhard Freiherr von Redwitz christoph.redw...@uni-rostock.de
Sent: 05 March 2015 15:29
To: R-sig-ecology@r-project.org
Subject: [R-sig-eco] vegan: goodness() and pRDA
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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