[R-sig-eco] Vegan: Question regarding adonis

[Pedro Neves]

Dear all:

I have a few questions regarding the use of PERMANOVA (adonis function 
in vegan) and maybe someone here might be able to help.

I want to use the adonis function to compare abundance data from 6 
locations at different times. I have 35 samples for each location at 
each time, totalling 805 observations.

My independent variables are Location (nested in Habitat type) and 
Campaign (nested in Season).

Now the questions are:

1 - regarding my replicates (the 35 samples for each location/time): 
they enter the analysis or I must calculate average them and use this 
average on the Permanova? If they enter the analysis (i.e. no average is 
needed) to I need to specify it as a factor in strata?

2 - Nested factors: I'm using a formula like this:

adonis(Myabund_matrix ~ Habitat/Location * Season/Campaign, 
strata=Location, data=Mydata_matrix)

Is this the correct approach? Do I need anything else in strata?

Thanks in advance for your attention.

All the best:


Pedro Neves


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