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 [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology