Hi everybody,
I’m in troubles with results I obtained using rda function of vegan package
and I would greatly appreciate some help.
I did a rda to assess if my matrix of species abundances (18 sites and 34
species) can be explained by my environmental matrix (18 sites and 5
variables). Abundances were transformed according hellinger equation
First I did a rda with all my environmental variables, and then did the
overall test. It was no significant.
myrda1<-rda(decostand(abund, "hellinger")~.,VarEnv)
anova(myrda1)
Permutation test for rda under reduced model
Model: rda(formula = decostand(abund, "hellinger") ~ VAR1 + VAR2 + Var3 +
Var4 + VAR5, data = VarEnv)
Df Var F N.Perm Pr(>F)
Model 5 0.062863 1.025 99 0.43
Residual 12 0.147195
I also did the test by margin (all pvalues were no significant), and by
axis (first axis significant)
anova(myrda1, by="axis")
Model: rda(formula = decostand(abund, "hellinger") ~ VAR1 + VAR2 + Var3 +
Var4 + VAR5, data = VarEnv)
Df Var F N.Perm Pr(>F)
RDA1 1 0.030016 2.4470 199 0.01 **
RDA2 1 0.013816 1.1263 99 0.29
RDA3 1 0.009770 0.7965 99 0.68
RDA4 1 0.006273 0.5114 99 0.84
RDA5 1 0.002989 0.2437 99 1.00
Residual 12 0.147195
On the plot, first axis is explained by Var1 and Var4
Since I was surprised by the results of the global test I tried a forward
selection. Only the Var4 was kept is the final model, and the test was now
significant. I also did backward selection ; it was the Var1 which was kept
is the final model, and the test was significant too.
So my question is, why the global test of the rda with all the environmental
variables is not significant while the test by “axis” is significant for the
first one (explain by variables Var1 and Var4) and while model selection
lead to significant test for Var1 or Var4 ?
I analyzed the VIF of the full model, and all were lower than 3
vif.cca(myrda1)
VAR1 VAR2 Var3 Var4 VAR5
2.573506 2.949139 2.209569 2.023914 1.854133
Thanks in advance for your help.
All the best.
Claire Della Vedova
--
View this message in context:
http://r-sig-ecology.471788.n2.nabble.com/troubles-with-global-test-of-rda-from-vegan-tp7578754.html
Sent from the r-sig-ecology mailing list archive at Nabble.com.
_______________________________________________
R-sig-ecology mailing list
R-sig-ecology@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
