Calculate beta diversity dissimilarities with or without rarefaction

Calculate beta diversity dissimilarities with or without rarefaction

Usage

calcBeta(
  asvtable = NULL,
  metadata = NULL,
  numRare = 400,
  method = "bray",
  category = NULL,
  minReads = 1000,
  ...
)

Arguments

asvtable

Input ASV table. Can be filtered with filtering()

metadata

Metadata input object

numRare

Number of rarefactions to perform. Set to 0 if you do not want to do any rarefication.

method

Dissimilarity index to use. See ?vegan::vegdist for more information.

category

Name in metadata column that you'd like to use

minReads

Minimum number of reads to keep a sample

...

allow passed arguments to nested functions

Value

A dissimilarity matrix

Examples

asvtable <- unsampled_example()$asvtable
metadata <- unsampled_example()$metadata
calcBeta(asvtable = asvtable, metadata = metadata, category = "host_sex", method = "bray")
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> Warning: function should be used for observed counts, but smallest count is 2
#> $dissimilarities
#>           1         2         3
#> 2 0.8518449                    
#> 3 0.9361599 0.9090784          
#> 4 0.7926446 0.8353664 0.9253335
#> 
#> $betadisper_res
#> 
#> 	Homogeneity of multivariate dispersions
#> 
#> Call: vegan::betadisper(d = averagedbc, group = metadata[[category]])
#> 
#> No. of Positive Eigenvalues: 3
#> No. of Negative Eigenvalues: 0
#> 
#> Average distance to median:
#> female   male 
#> 0.3963 0.4545 
#> 
#> Eigenvalues for PCoA axes:
#>  PCoA1  PCoA2  PCoA3 
#> 0.4744 0.3653 0.3130 
#> 
#> $pcoa_metadata
#> # A tibble: 4 × 10
#>   SampleID  LabID SampleType host_age host_sex Host_disease neg     PCoA1  PCoA2
#>   <chr>     <chr> <chr>         <int> <chr>    <chr>        <lgl>   <dbl>  <dbl>
#> 1 5080-MS-… part… Homo sapi…       33 female   healthy      FALSE  0.272   0.257
#> 2 5080-MS-… part… Homo sapi…       25 male     healthy      FALSE  0.0670 -0.515
#> 3 5348-MS-… part… Homo sapi…       27 male     COVID-19     FALSE -0.581   0.119
#> 4 5348-MS-… part… Homo sapi…       26 female   COVID-19     FALSE  0.242   0.140
#> # ℹ 1 more variable: PCoA3 <dbl>
#>