Dear everyone,
I'm analyzing the diversity of species in the diet of a wild animals (detected in feces). I would like to compare the diversity by gender, site and month. To do so, I will use alpha and beta diversity. However, I am puzzled while preparing the data in R. What I should define as a sample here, should be the site, the animal, the month-site-gender?
It's my first diversity analysis and it's not clear to me. I am following: Statistical Analysis of Microbiome Data with R and https://grunwaldlab.github.io/analysis_of_microbiome_community_data_in_r/index.html
Have a pleasant day,
alpha is the number of species in the diet, gamma can be gender or site, beta is then gamma/alpha
Thank you Andrew. The thing is when I compute the alpha diversity I have a measure by sample (individuals). When, I compute (in R) Beta diversity I get a dissimilarity matrix between each sample (individuals). Should I aggregate my data by site for example before running the beta diversity calculation in R?
A deep thank you for your valuable support. Cheers,Q.
alpha is the total number of plant species found in a site, irrespective of individuals, gender and even month (you need to measure across a season though). Then you can compare sites, because beta diversity is a measure of difference in composition of species of plants between locations.
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