Imagine I inventarized a forest with 28 plots. Do I calculate the Shannon-Index for each plot and take the average, or should I calculate the Shannon-Index over the whole population?
I use R and the vegan package. A example for clarification: http://txt.do/d0l0l (broken link) is the entire population and http://textuploader.com/d0l0q (broken link) the population divides by subplots.
My code is something like that:
shannon<-diversity(spac, index = "shannon") #plotwise mean(shannon)