| boot_cclasso | Boot cclasso |
| cclasso | Measure correlation by cclasso function |
| cclasso_sub | CCLasso function for single lambda |
| comp_by_deleting_random_knowns_t_v3 | Create bootstrap networks and compare network measures for... |
| create_abund_heatmap | Create heatmap of OTU abundance |
| cv_loss_cclasso | Cross validation loss of single lambda cclasso |
| degree_calc_f | Calculate and store degree, betweenness, and closeness scores... |
| filterTaxonMatrix | Filter taxa in an abundance matrix |
| get_back_counts_for_lineplotf | Find prevalence of known and MDM OTUs across a range of... |
| get_back_res_meeting_min_occ | Create phyloseq and igraph objects of taxa meeting certain... |
| get_bar_and_dens_class_interactions | Do node neighbor comparison for all taxa within network |
| get_cclasso_info | Get graph and networks using cclasso to measure correlation... |
| get_degree_df_wo_unk | Get degree df without unk |
| get_graph_wo_unk | Create igraph object without MDM nodes at each rank |
| get_hub_plots_all_ranks | Create 5 network plots with nodes sized by hub score, each... |
| get_net_plots_all_ranks | Create network plot, with nodes colored by each... |
| get_pearson_info | Get graph and networks using pearson to measure correlation... |
| get_sparcc_info | Get graph and networks using sparcc to measure correlation... |
| heatmap.3 | Create heatmap |
| make_mdt | Make melted dataframe of relative abundance of each taxa |
| make_prev_df | Make dataframe of taxa prevalence, abundance, and... |
| met_wo_unk | For each rank from Phylum to Genus, remove all MDM |
| orig_phylo_w_MDM_names | Create final phyloseq object with ambiguous, unassigned, and... |
| pipe | Pipe operator |
| plotnet_comp_v2 | Modified Plot_network function to use specified graph layout |
| vis_comp_net_checks | Analyze and visualize network measure changes, checking for... |
| vis_comp_net_meas_boxplots2 | Analyze and visualize network measure changes for Original,... |
