Function reference • tidyamplicons

All functions
`abundances()`	Extract the abundance table
`abundances_matrix()`	Return an abundances matrix
`add_alphas()`	Add alpha diversity measures
`add_cluster()`	Add cluster number
`add_codifab()`	Perform compositional differential abundance analysis
`add_copca()`	Add compositional principal components to the sample table
`add_diversity_measures()`	Add some alpha diversity measures
`add_jervis_bardy()`	Apply the taxon QC method of Jervis-Bardy
`add_lib_size()`	Add total abundance per sample
`add_logratios()`	Add logratios
`add_max_rel_abundance()`	Add the maximum relative abundance of taxa to the taxon table
`add_mean_rel_abundances()`	Add average relative abundances
`add_occurrences()`	Add taxon occurrences to the taxon table
`add_pcoa()`	Add first two dimensions of PCOA
`add_presence_counts()`	Add absolute occurrences of taxa to the taxon table
`add_rel_abundance()`	Add relative abundance to abundance table
`add_rel_occurrence()`	Add the relative occurrence of taxa to the taxon table
`add_sample_clustered()`	Add clustered sample order
`add_sample_tibble()`	Add sample table to the tidyamplicons object
`add_spike_ratio()`	Add spike ratio
`add_taxon_name()`	Create sensible names for the taxa and add to taxon table
`add_taxon_name_color()`	Create taxon names suitable for visualization with color. A rank can be supplied to aggregate colors higher than the current rank.
`add_taxon_tibble()`	Add taxon metadata to the tidyamplicons object
`add_total_rel_abundance()`	Add the total relative abundance of taxa to the taxon table
`aggregate_samples()`	Aggregate samples with identical values for all metadata
`aggregate_taxa()`	Aggregate taxa on a given taxonomic rank
`as_abundances()`	Convert matrix with abundances to tidy data frame
`as_abundances_matrix()`	Convert abundances tidy data frame to matrix.
`as_phyloseq()`	Convert tidyamplicons object to phyloseq object
`as_tidyamplicons()`	Convert phyloseq object to tidyamplicons object
`bar_plot()`	Return a bar plot of the samples
`bar_plot_ly()`	Return an interactive bar plot of the samples
`betas()`	Get beta diversity table
`change_id_samples()`	Change sample IDs to a given expression
`change_id_taxa()`	Change taxon IDs to a given expression
`classify_taxa()`	(Re)classify amplicon sequences
`codifab_plot()`	Generate a compositional differential abundance plot
`create_test_ta()`	Create a tidyamplicons object for testing/example purporses
`create_tidyamplicons()`	Initiate tidyamplicons object
`everything()`	Get all data in one single table
`filter_abundances()`	Filter the abundances
`filter_samples()`	Filter the samples
`filter_taxa()`	Filter the taxa
`get_abundances_extended()`	Synonym of `everything`.
`get_bar_plot()`	Return a bar plot of the samples
`get_betas()`	Get beta diversity table
`get_history_plot()`	Return a history plot of the samples
`get_numbers()`	Return some descriptive numbers
`get_rel_abundance_matrix()`	Return a relative abundance matrix
`history_plot()`	Return a history plot of the samples
`make_tidyamplicons()`	Create a tidyamplicons object from three tidy tables
`mean_rel_abundances()`	Get mean relative abundances of taxa in general or per condition
`merge_samples()`	Synonym of `aggregate_samples`.
`merge_taxa()`	Synonym of `aggregate_taxa`.
`merge_tidyamplicons()`	Merge two tidyamplicons objects.
`mutate_abundances()`	Create extra variables in the abundances table
`mutate_samples()`	Create extra variables in the sample table
`mutate_taxa()`	Create extra variables in the taxon table
`numbers()`	Return some descriptive numbers
`occurrences()`	Get occurrences of taxa in general or per condition
`pcoa_plot_ly()`	Return an interactive pcoa plot of the samples
`perform_adonis()`	Perform an adonis test
`process_abundance_selection()`	Apply an abundance filtering to the taxon table
`process_sample_selection()`	Apply a sample filtering to the taxon and abundance tables
`process_taxon_selection()`	Apply a taxon filtering to the abundance table
`rank_names()`	Return rank names associated with a tidyamplicons object
`rarefy()`	Rarefy the samples to a given number of reads
`read_tidyamplicons()`	Read community data written by tidyamplicons
`remove_empty_samples()`	Removes empty samples from the tidyamplicons object
`report_numbers()`	Report numbers
`reset_ids()`	Reset the taxon and sample IDs
`sample_plot()`	Return a visualization designed for a small number of samples
`samples()`	Extract the sample table
`select_abundances()`	Retain or remove a set of abundance variables
`select_samples()`	Retain or remove a set of sample variables
`select_taxa()`	Retain or remove a set of taxon variables
`set_rank_names()`	Set rank names for a tidyamplicons object
`taxa()`	Extract the taxon table
`taxon_counts_in_conditions()`	Get occurrences of taxa in general or in conditions
`tidy_phyloseq()`	Convert phyloseq object to tidyamplicons object
`tidyamplicons`	tidyamplicons: Functions to manipulate and visualize amplicon count data.
`trim_asvs()`	Trim all sequences
`update_id_names()`	Rename the "sample" and "taxon" columns to "sample_id" and "taxon_id"
`update_lib_sizes()`	Update library sizes in the lib_size table
`update_tidyamplicons()`	Update old tidyamplicons object to new one.
`write_tidyamplicons()`	Write community data in tidyamplicons format

Reference

All functions