I'm working with ecological community data collected from different sites and want to make comparisons between the sites using descriptors like richness, Shannon Weiner's diversity, and Simpson's evenness. There are some sites with multiple temporal replicates and others with just one sample. What is the best way to summarize the community data for sites with multiple replicates so they can be compared with the sites with only one sample? For example, the dataset looks something like this, where the values are counts of each species:
SiteA_Rep1 SiteA_Rep2 SiteA_Rep3 SiteB SiteC SiteD_Rep1 SiteD_Rep2 SpeciesA 1 4 2 0 2 0 6 SpeciesB 0 2 0 7 4 1 2 SpeciesC 7 6 3 6 2 3 0 ...
I am trying to summarize the data so that I have one count for each species at each site. I have tried taking the mean or median count for each species at a site with multiple replicates, but this inflates the richness because in effect I am increasing the sampling intensity at that site and increasing the chance that a rare species is encountered.
I have also looked at rarefaction methods for estimating richness, but I need the species counts for my other metrics.
Is there an ideal way to turn these replicates into one "sample" while preserving counts for each of the species?