Package overview

These are the functions that are accessible after loading the FuncDiv library in R. There is detailed documentation for each function that is part of the package, which you can access with ? in R (e.g., ?alpha_contrib_div). Essentially, alpha_contrib_div and beta_contrib_div are the main workflow functions, while the remaining accessible functions are supplementary tools.

• alpha_div_contrib - Function for computing contributional alpha diversity.

• beta_div_contrib - Function for computing contributional beta diversity.

• FuncDiv_alpha_metrics - List object containing alpha diversity metric functions as elements. Meant to be used by the alpha_div_contrib function, but can also be directly accessed by users.

• compute_alpha_div - Convenience function for computing alpha diversity functions present in FuncDiv_alpha_metrics.

• subset_func_and_abun_tables - Function for subsetting function copy number and taxa abundance tables to the same set of taxa. Will also remove any functions and/or samples that have no non-zero values after this step.

• contrib_to_multitab - Function for converting from the long-form contributional input format to the multi-table format (i.e., to the format with separate function and taxa abundance tables).

• multitab_to_contrib - Like contrib_to_multitab, but for conversion in the opposite direction.

• func_abun_crossproduct Convenience function for computing the cross-product between a function copy number and taxa abundance table. This corresponds to the community-wide function abundances present in each sample.