tidyamplicons v0.2.2

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_taxa for 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_tidyamplicons and write_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.exit in 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.

tidyamplicons v0.2.1

Minor updates and bug fixes:

• Messages of the type "Joining, by = ..." should now be very rare.
• The function aggregate_taxa now retains relative abundances if they are present.
• The function aggregate_taxa was updated to work with tidyr version 1.0.0.
• A bug was fixed in add_taxon_name.

tidyamplicons v0.2.0

This update introduces some code-breaking changes.

The biggest change is that the three tables are no longer linked by the variables sample and taxon, but by the internally created variables sample_id and taxon_id. You can apply this update to your existing tidyamplicons objects with the update_tidyamplicons function.

tidyamplicons v0.1.0

This is the first release of tidyamplicons!

tidyamplicons v0.0.0.9000

Update README.md