Population genetics graduate here. I'm currently working on using the R package 'vegan' to run a redundancy analysis for my data. I'm using the function vegan::anova.cca to run a permutation test to determine the significance of each environmental factor we are testing in the RDA to the RDA axis. Previously, when we tested for the significance of each RDA axis, we found that not only was RDA1 significant, but RDA2 was also significant in driving the genetic patterns we see in our RDA. Due to this, we not only wanted to show the environmental parameter correlations to RDA1 axis, but also to the second RDA axis, RDA2. So when running vegan:anova.cca with the option 'by = "terms"', I assumed this was testing each env. parameter against the 1st RDA axis - RDA1.
- Is this assumption correct? and 2. If so, is there a way I can easily test the exact same environmental parameters against only RDA2 (the second RDA axis?). I tried using 'first = FALSE' but got the same exact results as leaving this out of the command. I've looked around online but couldn't find a solution to this.
Any help would be greatly appreciated, thank you!!
Code:
param.sig <- anova.cca(sim.rda, by="terms", first = FALSE, parallel=getOption("mc.cores"))
param.sig