New functions:
- Added
classify_taxa: a function to (re)classify all or a subset of the amplicon sequences (if present), given a reference database. See?classify_taxafor more explanation or the reclassify_lactos project for a demonstration. - Added functions for compositional differential abundance analysis (codifab):
add_logratios,add_codifab,codifab_plot,add_copca. - Added
read_tidyampliconsandwrite_tidyamplicons. These functions read and write the three tidyamplicons tibbles from/to csv files. - Added
abundances_matrix, a function that returns the abundances as a matrix.
Bug fixes:
- Fixed wrong usage of
base::on.exitin multiple tidyamplicons functions (this became a problem in R version 4.1.1 and possibly earlier). - Fixed a bug in
rarefy.
Varia:
- Added at least very minimal documentation for each function.
- Removed the function
process_new_sample_name.