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
Alpha-diversity measure(s) to be included if not all. A vector of one or more of:
(logical) Also calculate sample richness estimates (Chao1 and ACE) as calculated by
Rarefy species richness to this value before calculating alpha diversity and/or richness. Passed directly as the
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:
Kasper Skytte Andersen email@example.com
Mads Albertsen MadsAlbertsen85@gmail.com
# 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 )#>#># Explore the results in the data frame # View(alphadiversityresult)