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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