data-raw/prep_data.R

In leffj/mctoolsr: Microbial Community Data Analysis Tools

library(mctoolsr)

map_fp = system.file('extdata', 'fruits_veggies_metadata.txt', 
                     package = 'mctoolsr')
tab_fp_biom = system.file('extdata', 'fruits_veggies_taxa_table_wTax.biom', 
                          package = 'mctoolsr')
tree_fp = system.file('extdata', 'fruits_veggies_taxa.tre', 
                      package = 'mctoolsr')

input = load_taxa_table(tab_fp = tab_fp_biom, map_fp = map_fp)
tree = load_tree(tree_fp)

## fruits_veggies
fruits_veggies = input
devtools::use_data(fruits_veggies, overwrite = TRUE)

## sumtax example data
sumtax_example_data = summarize_taxonomy(input, 2)
devtools::use_data(sumtax_example_data, overwrite = TRUE)

## OTU tree
fruits_veggies_OTUs_tree = tree
devtools::use_data(fruits_veggies_OTUs_tree, overwrite = TRUE)