Alpha diversity — alphaDiv • MicrobiomeDB

This function returns alpha diversity values for each sample.

Usage

alphaDiv(
  data,
  method = c("shannon", "simpson", "evenness"),
  verbose = c(TRUE, FALSE)
)

Arguments

data: AbundanceData object
method: string defining the the alpha diversity method. Accepted values are 'shannon','simpson', and 'evenness'
verbose: boolean indicating if timed logging is desired

Value

ComputeResult object

Examples

alphaDivOutput <- alphaDiv(
     getCollection(
  microbiomeData::DiabImmune, 
  "16S (V4) Genus (Relative taxonomic abundance analysis)"), 
     method = "shannon"
)
#> 
#> 2024-06-26 14:27:32.810508 Received df table with 3184 samples and 674 taxa.
#> 
#> 2024-06-26 14:27:32.952259 shannon alpha diversity computation complete.
#> 
#> 2024-06-26 14:27:32.967831 Alpha diversity computation completed with parameters method= shannon