Files in datelife

Scientific Data on Time of Lineage Divergence for Your Taxa

NEWS.md README.md R/use_calibrations_pathd8.R R/to_phylo_all.R R/lonely_functions.R R/calibrations_get.R R/result.R R/cacheauthors.R R/tree_add_dates.R R/datelife_internal.R R/tree_from_taxonomy.R R/print.R R/opentree_taxonomy_general.R R/summary.R R/datelife_summary.R R/opentree_taxonomy.R R/otol_tree.R R/use_calibrations_bladj_matched.R R/calibrations_extract.R R/data.R R/datelife_calibrations.R R/to_newick.R R/messages.R R/datelife_search.R R/datelife_query2.R R/get_species_from_ott.R R/calibrations_congruify.R R/bold_data.R R/datelife_use.R R/to_phylo.R R/datelife_sdm.R R/make_mrbayes_tree.R R/use_calibrations_treePL.R R/datelife_result.R R/calibrations_mrca.R R/calibrations_match.R R/groves.R R/opentree_chronograms.R R/bold_tree.R R/tree_processing.R R/uncertainty.R R/calibrations_use.R R/pkg_reports_functions.R R/matrix_to_table.R R/datelife_median.R R/make_bladj_tree.R R/tree_fix_brlen.R R/use_calibrations_bladj.R R/datelife_query_tnrs.R R/datelife_query.R inst/doc/fringiliidae.Rmd inst/doc/make_datelife_query.Rmd inst/doc/Getting_started_with_datelife.Rmd inst/doc/make_datelife_query.R inst/doc/making_bold_trees.Rmd inst/doc/fringiliidae.R inst/doc/Getting_started_with_datelife.R vignettes/fringiliidae.Rmd vignettes/make_datelife_query.Rmd vignettes/README.R vignettes/Getting_started_with_datelife.Rmd vignettes/making_bold_trees.Rmd man/results_list_process.Rd man/run.Rd man/subset2_taxa.Rd man/patristic_matrix_unpad.Rd man/input_process.Rd man/congruify_and_mrca_multiPhylo.Rd man/datelife_use.Rd man/get_goodmatrices.Rd man/datelife_result_variance_matrix.Rd man/dot-get_ott_lineage.Rd man/make_bladj_tree.Rd man/get_calibrations_datelifequery.Rd man/tnrs_match.Rd man/summarize_fossil_range.Rd man/contributor_cache.Rd man/is_datelife_query.Rd man/get_opentree_chronograms.Rd man/tree_check.Rd man/matrices_to_table.Rd man/use_calibrations_pathd8.Rd man/get_biggest_multiphylo.Rd man/update_datelife_cache.Rd man/patristic_matrix_MRCA.Rd man/get_valid_children.Rd man/extract_calibrations_phylo.Rd man/extract_calibrations_dateliferesult.Rd man/datelife_search.Rd man/run_mrbayes.Rd man/congruify_and_check.Rd man/get_mrbayes_node_constraints.Rd man/patristic_matrix_pad.Rd man/make_treebase_associations.Rd man/phylo_generate_uncertainty.Rd man/get_datelife_result.Rd man/get_taxon_summary.Rd man/get_subset_array_dispatch.Rd man/get_bold_data.Rd man/use_calibrations.Rd man/phylo_tiplabel_underscore_to_space.Rd man/summarize_congruifiedCalibrations.Rd man/update_all_cached.Rd man/make_overlap_table.Rd man/check_conflicting_calibrations.Rd man/tree_add_outgroup.Rd man/datelife_result_sdm_phylo.Rd man/tree_get_singleton_outgroup.Rd man/birds_and_cats.Rd man/classification_paths_from_taxonomy.Rd man/get_ott_lineage.Rd man/make_mrbayes_runfile.Rd man/felid_gdr_phylo_all.Rd man/patristic_matrix_to_phylo.Rd man/extract_ott_ids.Rd man/datelife_result_study_index.Rd man/get_ott_clade.Rd man/phylo_subset_both.Rd man/phylo_has_brlen.Rd man/summary.datelifeResult.Rd man/get_datelife_result_datelifequery.Rd man/get_otol_synthetic_tree.Rd man/get_fossil_range.Rd man/datelife_use_datelifequery.Rd man/felid_sdm.Rd man/tree_node_tips.Rd man/make_contributor_cache.Rd man/datelife_result_sdm_matrix.Rd man/summary_matrix_to_phylo_all.Rd man/tree_add_dates.Rd man/sample_trees.Rd man/congruify_and_mrca_phylo.Rd man/datelife_authors_tabulate.Rd man/phylo_prune_missing_taxa.Rd man/get_all_calibrations.Rd man/pick_grove.Rd man/get_tnrs_names.Rd man/phylo_get_subset_array.Rd man/datelife_result_median.Rd man/match_all_calibrations.Rd man/patristic_matrix_array_subset.Rd man/choose_cluster.Rd man/missing_taxa_check.Rd man/phylo_get_node_numbers.Rd man/use_calibrations_bladj.Rd man/patristic_matrix_name_reorder.Rd man/datelife_result_median_matrix.Rd man/recover_mrcaott.Rd man/clean_tnrs.Rd man/opentree_chronograms.Rd man/clean_taxon_info_children.Rd man/get_ott_children.Rd man/plant_bold_otol_tree.Rd man/is_n_overlap.Rd man/make_datelife_query2.Rd man/make_mrbayes_tree.Rd man/get_calibrations_vector.Rd man/make_all_associations.Rd man/make_otol_associations.Rd man/summarize_datelife_result.Rd man/threebirds_dr.Rd man/make_treebase_cache.Rd man/map_nodes_ott.Rd man/get_dated_otol_induced_subtree.Rd man/patristic_matrix_array_split.Rd man/phylo_get_subset_array_congruify.Rd man/clean_ott_chronogram.Rd man/phylo_congruify.Rd man/check_ott_input.Rd man/get_all_descendant_species.Rd man/is_datelife_result_empty.Rd man/use_all_calibrations.Rd man/treebase_cache.Rd man/tree_get_node_data.Rd man/subset2_search.Rd man/use_calibrations_each.Rd man/filter_for_grove.Rd man/make_bold_otol_tree.Rd man/phylo_to_patristic_matrix.Rd man/tree_add_nodelabels.Rd man/use_calibrations_bladj.matchedCalibrations.Rd man/patristic_matrix_array_phylo_congruify.Rd man/patristic_matrix_array_congruify.Rd man/patristic_matrix_taxa_all_matching.Rd man/summarize_summary_matrix.Rd man/use_calibrations_treePL.Rd man/datelife_result_MRCA.Rd man/is_good_chronogram.Rd man/build_grove_matrix.Rd man/patristic_matrix_to_newick.Rd man/cluster_patristicmatrix.Rd man/matrix_to_table.Rd man/tree_from_taxonomy.Rd man/get_opentree_species.Rd man/tree_fix_brlen.Rd man/summary_patristic_matrix_array.Rd man/make_datelife_query.Rd man/get_best_grove.Rd man/some_ants_datelife_result.Rd man/patristic_matrix_list_to_array.Rd man/message_multiphylo.Rd man/force_ultrametric.Rd man/summary_matrix_to_phylo.Rd man/summary.matchedCalibrations.Rd man/date_with_pbdb.Rd man/problems.Rd man/relevant_curators_tabulate.Rd man/build_grove_list.Rd man/patristic_matrix_array_subset_both.Rd man/patristic_matrix_name_order_test.Rd man/phylo_tiplabel_space_to_underscore.Rd man/make_sdm.Rd man/mrca_calibrations.Rd man/phylo_check.Rd