CODEWITHSUNDEEP
rvegan
Stevestingray
Stevestingray

Reputation: 453

Calculate Gamma diversity over complete dataset using Vegan package in R

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

Upvotes: 1

Views: 1006

Answers (1)

Jari Oksanen
Jari Oksanen

Reputation: 3682

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

Upvotes: 2

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