I have some datasets for which i want to calculate gamma diversity as the Shannon H index.
Example dataset:
Site SpecA SpecB SpecC
1 4 0 0
2 3 2 4
3 1 1 1
Calculating the alpha diversity is as follows:
vegan::diversity(df, index = "shannon")
However, i want this diversity function to calculate one number for the complete dataset instead of for each row. I can't wrap my head around this. My thought is that i need to write a function to merge all the columns into one and taking the average abundance of each species, thus creating a dataframe with one site contaning all the species information:
site SpecA SpecB SpecC
1 2.6 1 1.6
This seems like a giant workaround for something that could be done with some existing functions, but i don't know how. I hope someone can help in creating this dataframe or using some other method to use the diversity() function over the complete dataframe.
Regards
library(vegan)
data(BCI)
diversity(colSums(BCI)) # vector of sums is all you need
## vegan 2.6-0 in github has 'groups' argument for sampling units
diversity(BCI, groups = rep(1, nrow(BCI))) # one group, same result as above
diversity(BCI, groups = "a") # arg 'groups' recycled: same result as above