Calculate alpha-diversity indices for each sample and combines with the metadata.

amp_alphadiv(data, measure = NULL, richness = FALSE, rarefy = NULL)



(required) Data list as loaded with amp_load.


Alpha-diversity measure(s) to be included if not all. A vector of one or more of:

  • "observed"

  • "shannon"

  • "simpson"

  • "invsimpson"


(logical) Also calculate sample richness estimates (Chao1 and ACE) as calculated by estimateR. (default: FALSE)


Rarefy species richness to this value before calculating alpha diversity and/or richness. Passed directly as the sample argument to rrarefy. (default: NULL)


A data frame.


The alpha-diversity indices are calculated per sample using the vegan function diversity, where the read abundances are first rarefied using rrarefy by the size of the rarefy argument. Refer to the vegan documentation for details about the different indices and how they are calculated. If no measure(s) are chosen, all diversity indices will be returned.


McMurdie, P.J. & Holmes, S. (2014). Waste not, want not: Why rarefying microbiome data is inadmissible. PLoS Comput Biol 10(4): e1003531. DOI:10.1371/journal.pcbi.1003531

See also


Kasper Skytte Andersen

Mads Albertsen


# Load example data data("AalborgWWTPs") # Subsample/rarefy to 20000 reads and then calculate # Shannon and Simpson alpha-diversity indices alphadiversityresult <- amp_alphadiv(AalborgWWTPs, measure = c("shannon", "simpson"), rarefy = 20000 )
#> The following sample(s) have not been rarefied (less than 20000 reads): #> 16SAMP-703, 16SAMP-739, 16SAMP-10907
# Explore the results in the data frame # View(alphadiversityresult)