abun_isometric_log_ratios |
Compute isometric log ratio based on abundance of feature sets |
compute_node_balances |
Compute balances at tree nodes. |
filter_rare_table_cols |
Filters out columns of dataframe based on number of proportion of non-zero cells |
genome_content_phylo_regress |
Phylogenetic regression of input vector against function presence/absence. |
node_taxa |
Determine taxa labels of tips on each side of a node |
phylolm_summary |
Wrapper for running phylogenetic regression with phylolm |
POMS_pipeline |
Main function to run POMS pipeline |
prep_func_node_info |
Get node indices of FSN and BSN categories across tree for a given function |
prevalence_norm_logit |
Compute additive smoothed prevalence of features (e.g, taxa), restricted to samples of a particular metadata category. |
specificity_scores |
Compute shrunken specificity score of a feature, which represents how the presence of a feature is associated with a given sample grouping. |
subset_by_col_and_filt |
Subset dataframe by column names and then post-filter |