[R-sig-eco] Nested Permanova with repeated measures

[Paul Moquin]

Wow- Thank you so much for this!!- I do however have a little confusion on
this part- which is well ,most of it (-:


"If you want to include all weeks and examine the between-subjects effects,
then you need to use betadisper() to get the centroid across all 11 weeks
for each microcosm. "

I do indeed want to us all weeks so I did this to get the centroids for
each mesocosm:

*mc.centroids<-betadisper(vegdist(community, method="bray"),mesocosm) #get
mesocosm centroids *
*correct?  and now *you say "Using a grouping variable (let's call it
block.treatment.combo), you can get a new matrix made up of 12 centroids,
one for each subject (mesocosm; let's call it community.centroids.among.weeks).
Using this matrix of centroids, run the following model:

Community.centroids.among.weeks ~ treatment + block"

I'm afraid I was not able to follow you here! Could you provide the code
you would use there?

	[[alternative HTML version deleted]]