load_data: This function wrangles the filtered ABRP data and metadata
In kimberlyroche/rulesoflife:

load_data

R Documentation

This function wrangles the filtered ABRP data and metadata

Description

This function wrangles the filtered ABRP data and metadata

Usage

load_data(
  tax_level = "ASV",
  host_sample_min = 75,
  count_threshold = 1,
  sample_threshold = 0.2,
  alr_median = FALSE
)

Arguments

`tax_level`	taxonomic level at which to agglomerate data
`host_sample_min`	minimum sample number for host inclusion in the filtered data set
`count_threshold`	minimum count for taxon inclusion in the filtered data set
`sample_threshold`	minimum proportion of samples within each host at which a taxon must be observed at or above count_threshold
`alr_median`	if TRUE, uses the taxon with the median coefficient of variation in relative abundance as the ALR reference taxon, otherwise uses the taxon in the last index in the count table

Details

Together count_threshold and sample_threshold specify a minimum representation for a taxon. Taxa below this threshold will be grouped together into an <NA> category.