Files in reptalex/dendromap
dendromap: R package for using time-scaled reference trees to scale microbial phylogenies.
.gitignore
DESCRIPTION
NAMESPACE
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
data/birds/PTrees.Rdata
data/birds/bird_conts.Rdata
data/birds/bird_dendromap
data/birds/bird_dendromap_nonzero_contingencies
data/birds/bird_dendromap_workspace
data/birds/continental_tree
data/edendromap_birds_workspace
data/primates/Reduced_mapping_4persp_nohyb_RC2036.txt
data/primates/basalMax_workspace
data/primates/big_graph
data/primates/big_graph2
data/primates/big_graph3
data/primates/dendromap_P1e-3_threshold
data/primates/dendromap_P5e-3_threshold
data/primates/final.seqs.fa
data/primates/final.seqs_aligned.meg
data/primates/final.withtax.biom
data/primates/final.withtax.min10.biom
data/primates/final.withtax.min10.summary.txt
data/primates/final_withtax_min10.meg
data/primates/final_withtax_min10.tre
data/primates/furcated_host_tree.tre
data/primates/monkey_subtree.tre
data/primates/primate_dendromap_guts_workspace
data/primates/primate_tree_376_taxa-chronogram_newick.tre
docs/Jacob_node_dendromap_thoughts.docx
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/.DS_Store
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
src/bifurcations.c
src/bifurcations.o
src/dendromap.dll
src/dendromap_init.c
src/dendromap_init.o
