Files in reptalex/dendromap

dendromap: R package for using time-scaled reference trees to scale microbial phylogenies.

Old_R/Path_scripts.R Old_R/ancestorTable.R Old_R/basalMax.R Old_R/basalMaxima.R Old_R/check_joinable.R Old_R/countDescendants.R Old_R/dendromap.R Old_R/dendromap2.R Old_R/dendromap_edge.R Old_R/depthDraw.R Old_R/disjointNodeset.R Old_R/edge_dendromap_fcns.R Old_R/filter_winner.R Old_R/findLineageTable.R Old_R/findNodeSeq.R Old_R/find_joinables.R Old_R/find_lineages.R Old_R/getFstat.R Old_R/getIndexSets.R Old_R/idComparables.R Old_R/labelledChildren.R Old_R/makeDataset.R Old_R/makeDescendantTable.R Old_R/makeNodeMap.R Old_R/makeRCmap.R Old_R/makeRCtable.R Old_R/makeRowColSet.R Old_R/manifestChildren.R Old_R/manifestRowChildren.R Old_R/matchAncestors.R Old_R/matchDescendants.R Old_R/max_clique_SA.R Old_R/nodeBank.R Old_R/pathViz.R Old_R/plot.dendromap.R Old_R/plot.treesim.R Old_R/print.dendromap.R Old_R/rc_seqs.R Old_R/rootpath.R Old_R/scanFstats.R Old_R/scanFstats_e.R Old_R/summarize_lineage.R Old_R/treeBasis.R Old_R/treeMap.R Old_R/treeSim.R Old_R/warpTree.R R/anc_desc_table.R R/assemble_lineage.R R/assemble_lineage_par.R R/basal_dominance_filter.R R/contrast_vector.R R/dendroMap.R R/edge_ancestors.R R/edge_contrasts.R R/edge_registry.R R/edge_tips.R R/filter_stats.R R/get_lineage.R R/get_lineage_par.R R/get_lineages_and_stats.R R/get_phylo_groups.R R/get_rc_relations.R R/global_Fstat.R R/grow_lineage.R R/incompatible_descendants.R R/lineage_boxes.R R/lineage_plot.R R/lineage_stats.R R/lstat.R R/make_rc_table.R R/merge_twin_sisters.R R/plot.dendromap.R R/predict.dendromap.R R/rdendromap.R R/scan_Fstats.R R/simplify_rc_table.R R/simulate.dendromap.R man/anc_desc_table.Rd man/assemble_lineage.Rd man/basal_dominance_filter.Rd man/contrast_vector.Rd man/dendromap.Rd man/edge_ancestors.Rd man/edge_contrasts.Rd man/edge_registry.Rd man/edge_tips.Rd man/filter_stats.Rd man/get_lineage.Rd man/get_lineage_par.Rd man/get_lineages_and_stats.Rd man/get_phylo_groups.Rd man/get_rc_relations.Rd man/global_Fstat.Rd man/grow_lineage.Rd man/incompatible_descendants.Rd man/lineage_boxes.Rd man/lineage_plot.Rd man/lineage_stats.Rd man/lstat.Rd man/make_rc_table.Rd man/merge_twin_sisters.Rd man/plot.dendromap.Rd man/predict.dendromap.Rd man/rdendromap.Rd man/scan_Fstats.Rd man/simplify_rc_table.Rd scripts/F_stat_scanning.R scripts/Manifestation_Sequence_Search.R scripts/Null_distribution_simulations.R scripts/amphibians/amphib_cont_assoc.R scripts/amphibians/amphib_range_tree_harmonization.R scripts/amphibians/get_richness_raster.R scripts/amphibians/make_rasters.R scripts/amphibians/richness_plotting.R scripts/aves_microbiome_phylofactorization.R scripts/benchmarking.R scripts/big graph cliques.R scripts/bird_biogeography.R scripts/bird_continental_tree.R scripts/bird_edge_dendromap.R scripts/dendromap_guts.R scripts/edge_dendromap.R scripts/edge_dendromap2.R scripts/edgedm_treesim_making.R scripts/greedy_scaffold_construction.R scripts/making rc-mapping dendromap traversal.R scripts/peruse_bird_dendromap.R scripts/primate_dendromap_guts.R scripts/primate_dendromapping.R scripts/primates_analysis.R scripts/speeding_up_algo.R