Dear list,
I am looking for some pointers on how to use the anova.cca function in
the vegan package to test the significance of predictors in a redundancy analysis
(RDA).
Let's say that I have a simple rda, where "dep" is a 30x3 matrix with
the observations, and "indep" is a 30x6 matrix with the predictors. I
want to figure out which of the predictors are signficant. So I do
Then I do
anova.cca(myrda1,by="terms")
And I find out that v1,v2,v3, and v6 are signficiant (e.g. Pr(>F)
<0.05. So far so good. But anova.cca does a permutation test of the
predictors in the order they are in the model. So I rerun the model
changing the order of the variables:
Now, v2, v3, v5 and v6 are significant, but v1 is not anymore.
I can also run anova.cca "by margin", which tests the marginal effect of
each variable. If I do
I get in both cases that variables v2, v5 and v6 are significant.
Also, instad of using anova.cca, I can use the "forward.sel" function in
the "packfor" package to identify a subset of variables that explain the same
amount of variability than the full model. If I do this by doing
library(packfor)
r2 <- RsquareAdj(ra)$adj.r.squared
red <-forward.sel(dep,indep,adjR2thresh=r2)
I obtain a reduced model with variables v2, v5, v6, which matches the
significant variables obtained when doing anova.cca with the "by=margin"
option. So intuitively, it seems that testing the marginal effect of each
variable (i.e. using "by=margin") is the correct way to detect the
dependent variables that do have an effect on the indpendent variables.
Is this correct? Any insights will be welcomed!
Julian
Julian Mariano Burgos, PhD
Hafranns?knastofnun/Marine Research Institute
Sk?lagata 4, 121 Reykjav?k, Iceland
S?mi/Telephone : +354-5752037
Br?fs?mi/Telefax: +354-5752001
Netfang/Email: julian at hafro.is