Function reference • animalcules

All functions
`alpha_div_boxplot()`	Alpha diversity boxplot
`alpha_div_test()`	Get alpha diversity
`counts_to_logcpm()`	Covert a counts table to a relative abundances table
`counts_to_relabu()`	Covert a counts table to a relative abundances table
`df_char_to_factor()`	Factorize all categorical columns
`differential_abundance()`	Differential abundance analysis
`dimred_pca()`	Dimensionality reduction through PCA
`dimred_pcoa()`	Dimensionality reduction through PCoA
`dimred_umap()`	Dimensionality reduction through PCA
`dimred_tsne()`	Dimensionality reduction through t-SNE
`diversities()`	Get alpha diversity
`diversities_help()`	Get alpha diversity
`diversity_beta_boxplot()`	Beta diversity boxplot
`diversity_beta_heatmap()`	Beta diversity heatmap
`diversity_beta_NMDS()`	Beta diversity NMDS plot
`diversity_beta_test()`	Perform a beta diversity test
`do_alpha_div_test()`	Alpha diversity statistical test
`filter_categorize()`	Categorize continuous variables
`filter_summary_bar_density()`	Data visualization by bar plot / density plot
`filter_summary_pie_box()`	Data visualization by pie chart / box plot
`find_biomarker()`	Identify biomarkers
`find_taxon_mat()`	Find the Taxonomy Information Matrix
`find_taxonomy()`	Find the taxonomy for unlimited tids
`find_taxonomy_300()`	Find the taxonomy for maximum 300 tids
`gini_simpson()`	Get alpha diversity using gini
`grep_tid()`	Greps the tid from the given identifier string
`inverse_simpson()`	Get alpha diversity using inverse simpson
`is_categorical()`	Check if object is categorical
`is_integer0()`	check if integer(0)
`is_integer1()`	check if integer(1)
`mae_pick_organisms()`	Modify organisms of multi-assay experiment object
`mae_pick_samples()`	Modify samples of multi-assay experiment object
`pct2str()`	Converts decimal percentage to string with specified digits
`percent()`	Format decimals to percentages
`read_pathoscope_data()`	Reads the data from PathoScope reports and returns a list of final guess relative abundance and count data
`relabu_barplot()`	Plot bar plots of sample and group level relative abundance
`relabu_boxplot()`	Plot boxplots comparing different organism prevalence across conditions
`relabu_heatmap()`	Plot heatmap of sample level counts in logcpm
`run_animalcules()`	Run animalcules shiny app
`shannon()`	Get alpha diversity using shannon
`simpson_index()`	Get alpha diversity using simpson
`upsample_counts()`	Upsample a counts table to a higher taxon level
`write_to_biom()`	Output biom

Reference

All functions