Table 1. Functions included within the ranacapa package.
| Name | Description |
|---|---|
| scrub_seqNum_column | Removes any "xxx_seq_number" columns from the input taxonomy file if present
(depends on which version of Anacapa was used to assign taxonomy) |
| scrub_taxon_paths | Replaces empty cells in input taxonomy tables with “Unknown” |
| validate_input_files | Verifies that the input taxonomy file and input mapping file meet specifications |
| convert_biom_to_taxon_table | Converts a phyloseq-imported biom table into an Anacapa-formatted taxonomy
table |
| group_anacapa_by_taxonomy | Summarizes a site-abundance table from the Anacapa pipeline to each unique
taxon |
| categorize_continuous_vector | Categorizes a continuous vector into low, medium, and high |
| convert_anacapa_to_phyloseq | Converts a site-abundance table from the Anacapa pipeline and the associated
metadata file into a phyloseq object |
| vegan_otu | Creates a community matrix in the vegan package style using a phyloseq object
and an otu_table object |
| custom_rarefaction | Rarefies a phyloseq object to a custom sample depth and with a given number of
replicates |
| pairwise_adonis 1 | Wrapper function for multilevel pairwise comparison |
| ggrare 2 | Makes a rarefaction curve using ggplot2 |
| runRanacapaApp | Runs the ranacapa Shiny app with tabs for interactive visualizations and statistical
analyses |
1 adopted from https://github.com/pmartinezarbizu/pairwiseAdonis (GPL-3 License)
2 adopted from https://github.com/mahendra-mariadassou/phyloseq-extended (GPL-3 License)