This function consumes OTU table(s) and (optionally) a taxonomic rank, then extracts the classification of each OTU at the given taxonomic rank, groups by classification at the given rank, removes all groups with only 0 counts, optionally removes all unclassified groups, sorts groups based on abundance, and then returns the transpose.
This function consumes an OTU table and its associated metadata, and creates a plot showing how the collections of taxonomic groups, as well as metadata factors, evolve over time.
A properly formatted taxonomy column of an otu table is critical for RAM functions to run properly. The taxonomy column of an otu table is composed of taxonomic lineages for otuIDs. RAM accept 7 ranks, including kingdom, phylum, class, order, family, genus and species, sub ranks are not supported. Taxa names at each rank should have prefix as "k__", "p__", "c__", "o__", __", "g__", and "s__", each rank should be separated by "; ", i.e. a semi colon and a white space, NOT just ";". This function will check the format of the taxonomy column of the input otu table and give suggetions that whether or not it needs to be reformatted using reformat.taxonomy of RAM. However, RAM does accept missing ranks in lineages, as long as each rank is separated by "; " with proper prefix.
This function consumes an OTU table, and a vector containing taxnomic ranks, then returns what percent of OTUs in the given table are classified at each taxonomic rank.
This function consumes an OTU table and returns a new OTU table where the taxonomic classifications which are unidentified, unclassified, incertae sedis, or simply missing, are replaced with a more descriptive entry.
In all RAM functions requiring the user to input a taxonomic rank, three different formats for this taxon are accepted. All of these formats are simple character vectors (strings), and are provided for readability and convenience. The user only needs to specify any single element from any of the formats below. The formats are as follows:
RAM provides some customized ggplot themes to spice up your plots for presentations, but some of these addtional features might be distractive and not be ideal for publications
This function consumes an ecology data set, metadata factors, and graphing options, then produces a plot showing the vegan::cca or vegan::rda analysis.
providing 
.