Man pages for reptalex/dendromap
dendromap: R package for using time-scaled reference trees to scale microbial phylogenies.
| anc_desc_table | Get ancestor-descendant relations a given rc pair |
| assemble_lineage | Plot dendromap object |
| basal_dominance_filter | Remove all (r,c) such that P(r,c)>P(r',c) for some descendant... |
| contrast_vector | Internal function for computing an ilr balancing element... |
| dendromap | Coarse-grain dataset, X, based on discovered lineage |
| edge_ancestors | get path of ancestral edges all the way to, but not... |
| edge_contrasts | Create edge contrast vectors for tree |
| edge_registry | Make registry of edges and number of descendants for quick... |
| edge_tips | Table of edges and max/min values of descendant tips |
| filter_stats | Plot dendromap object |
| get_lineage | Build lineage from a given rc_index, using only P <= p_thresh |
| get_lineage_par | Build lineage from a given rc_index, using only P <= p_thresh |
| get_lineages_and_stats | Get lineages with all lineage F-statistics |
| get_phylo_groups | Get list of groups defined by phylogeny |
| get_rc_relations | Get all ancester-descendant relations of rc pairs |
| global_Fstat | Extract global F statistic for several Lineages |
| grow_lineage | grow_lineage from row/col edge pair. internal function for... |
| incompatible_descendants | Find descendant rc_indexes incompatible with input rc_index |
| lineage_boxes | Coarse-grain dataset, X, based on discovered lineage |
| lineage_plot | Focused of particular lineage |
| lineage_stats | Extract F statistics for all lineages |
| lstat | Extract F statistic for a given lineage |
| make_rc_table | Make table of row tree,column tree edge pair statistics |
| merge_twin_sisters | Identify sister row edges with same column edge association &... |
| plot.dendromap | Plot dendromap object |
| predict.dendromap | Predict dataset from dendromap object |
| rdendromap | Random dendromap object |
| scan_Fstats | Scan P-value thresholds, computing global F-statistic for... |
| simplify_rc_table | Remove (r,c) pairs without ancestors/descendants, and impose... |
