Package overview

These are the functions that are accessible after loading the POMS 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., ?POMS_pipeline). Essentially POMS_pipeline is the main function, while the others are mainly quick utility functions to help pre- and post-process the workflow data. There are also several functions for running phylogenetic regression and to compute metrics as descibed originally as part of the phylogenize package.

• POMS_pipeline - Main function to run the POMS workflow.

• abun_isometric_log_ratios - Compute isometric log ratio based on abundance of feature sets.

• compute_node_balances - Compute balances at tree nodes.

• node_taxa - Determine taxa labels of tips on each side of a node.

• prep_func_node_info - Get node indices of function-significant node and balance-significant node categories across tree for a given function.

• filter_rare_table_cols - Filters out columns of dataframe based on number of proportion of non-zero cells.

• subset_by_col_and_filt - Subset dataframe by column names and then post-filter.

• phylolm_summary - Convenience function for running phylogenetic regression with the phylolm R package based on specified response and dependent variable input vectors.

• genome_content_phylo_regress - Function that applies phylolm_summary based on a given response variables and all functions in a specified genome function copy number table.

• prevalence_norm_logit - Function for computing the prevalence scores introduced in phylogenize. Note that this code is a minor modification from the R implementation of phylogenize.

• specificity_scores - Function for computing the environmental specificity scores introduced in phylogenize. Note that this code is a minor modification from the R implementation of phylogenize.