phylotastic/datelife
Scientific Data on Time of Lineage Divergence for Your Taxa

Package index
Search the phylotastic/datelife package
Vignettes
Functions
314
Source code
90
Man pages
152
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phylotastic/datelife: Scientific Data on Time of Lineage Divergence for Your Taxa
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API

API for phylotastic/datelife
Scientific Data on Time of Lineage Divergence for Your Taxa

Global functions
.get_ott_lineage Man page Source code
birds_and_cats Man page
build_grove_list Man page Source code
build_grove_matrix Man page Source code
check_conflicting_calibrations Man page Source code
check_ott_input Man page Source code
choose_cluster Man page Source code
classification_paths_from_taxonomy Man page Source code
clean_ott_chronogram Man page Source code
clean_taxon_info_children Man page Source code
clean_tnrs Man page Source code
cluster_patristicmatrix Man page Source code
congruify_and_check Man page Source code
congruify_and_mrca_multiPhylo Man page Source code
congruify_and_mrca_phylo Man page Source code
contributor_cache Man page
date_with_pbdb Man page Source code
datelife Man page
datelife_authors_tabulate Man page Source code
datelife_calibrations Man page
datelife_query_get_spp Source code
datelife_result_MRCA Man page Source code
datelife_result_data_frame Source code
datelife_result_html Source code
datelife_result_median Man page Source code
datelife_result_median_and_sdm Source code
datelife_result_median_matrix Man page Source code
datelife_result_newick_all Source code
datelife_result_phylo_all Source code
datelife_result_sdm_matrix Man page Source code
datelife_result_sdm_phylo Man page Source code
datelife_result_study_index Man page Source code
datelife_result_variance_matrix Man page Source code
datelife_search Man page Source code
datelife_use Man page Source code
datelife_use_datelifequery Man page Source code
extract_calibrations_dateliferesult Man page Source code
extract_calibrations_phylo Man page Source code
extract_ott_ids Man page Source code
extract_ott_ids.default Man page Source code
felid_gdr_phylo_all Man page
felid_sdm Man page
filter_for_grove Man page Source code
force_ultrametric Man page Source code
get_all_calibrations Man page Source code Source code
get_all_descendant_species Man page Source code
get_best_grove Man page Source code
get_biggest_multiphylo Man page Source code
get_bold_data Man page Source code
get_calibrations_datelifequery Man page Source code
get_calibrations_vector Man page Source code
get_dated_otol_induced_subtree Man page Source code
get_datelife_result Man page Source code
get_datelife_result_datelifequery Man page Source code
get_fossil_range Man page Source code
get_goodmatrices Man page Source code
get_mrbayes_node_constraints Man page Source code
get_opentree_chronograms Man page Source code
get_opentree_species Man page Source code
get_otol_chronograms Man page
get_otol_synthetic_tree Man page Source code
get_ott_children Man page Source code
get_ott_clade Man page Source code
get_ott_lineage Man page Source code
get_subset_array_dispatch Man page Source code
get_taxon_summary Man page Source code
get_tnrs_names Man page Source code
get_valid_children Man page Source code
input_process Man page Source code
is_datelife_query Man page Source code
is_datelife_result_empty Man page Source code
is_good_chronogram Man page Source code
is_n_overlap Man page Source code
make_all_associations Man page Source code
make_bladj_tree Man page Source code
make_bold_otol_tree Man page Source code
make_contributor_cache Man page Source code
make_datelife_query Man page Source code
make_datelife_query2 Man page Source code
make_mrbayes_runfile Man page Source code
make_mrbayes_tree Man page Source code
make_otol_associations Man page Source code
make_overlap_table Man page Source code
make_sdm Man page Source code
make_treebase_associations Man page Source code
make_treebase_cache Man page Source code
map_nodes_ott Man page Source code
match_all_calibrations Man page Source code
matrices_to_table Man page Source code
matrix_to_table Man page Source code
message_multiphylo Man page Source code
missing_taxa_check Man page Source code
mrca_calibrations Man page Source code
numeric_vector_to_html_row Source code
opentree_chronograms Man page
patristic_matrix_MRCA Man page Source code
patristic_matrix_array_congruify Man page Source code
patristic_matrix_array_phylo_congruify Man page Source code
patristic_matrix_array_split Man page Source code
patristic_matrix_array_subset Man page Source code
patristic_matrix_array_subset_both Man page Source code
patristic_matrix_list_to_array Man page Source code
patristic_matrix_name_order_test Man page Source code
patristic_matrix_name_reorder Man page Source code
patristic_matrix_pad Man page Source code
patristic_matrix_sample Source code
patristic_matrix_subset Source code
patristic_matrix_taxa_all_matching Man page Source code
patristic_matrix_to_newick Man page Source code
patristic_matrix_to_phylo Man page Source code
patristic_matrix_unpad Man page Source code
phylo_check Man page Source code
phylo_congruify Man page Source code
phylo_generate_uncertainty Man page Source code
phylo_get_node_numbers Man page Source code
phylo_get_subset_array Man page Source code
phylo_get_subset_array_congruify Man page Source code
phylo_has_brlen Man page Source code
phylo_prune_missing_taxa Man page Source code
phylo_subset_both Man page Source code
phylo_tiplabel_space_to_underscore Man page Source code
phylo_tiplabel_underscore_to_space Man page Source code
phylo_to_patristic_matrix Man page Source code
pick_grove Man page Source code
plant_bold_otol_tree Man page
problems Man page
recover_mrcaott Man page Source code
relevant_age_quantiles Source code
relevant_curators_tabulate Man page Source code
results_list_process Man page Source code
run Man page Source code
run_mrbayes Man page Source code
sample_trees Man page Source code
some_ants_datelife_result Man page
subset2_search Man page
subset2_taxa Man page
summarize_congruifiedCalibrations Man page Source code
summarize_datelife_result Man page Source code
summarize_fossil_range Man page Source code
summarize_summary_matrix Man page Source code
summary.datelifeResult Man page Source code
summary.matchedCalibrations Man page Source code
summary_matrix_to_phylo Man page Source code
summary_matrix_to_phylo_all Man page Source code
summary_patristic_matrix_array Man page Source code
threebirds_dr Man page
tnrs_match Man page Source code
tnrs_match.default Man page Source code
tnrs_match.phylo Man page Source code
treePL.phylo Source code
tree_add_dates Man page Source code
tree_add_nodelabels Man page Source code
tree_add_outgroup Man page Source code
tree_check Man page Source code
tree_fix_brlen Man page Source code
tree_from_taxonomy Man page Source code
tree_get_node_data Man page Source code
tree_get_singleton_outgroup Man page Source code
tree_node_tips Man page Source code
treebase_cache Man page
update_all_cached Man page Source code
update_datelife_cache Man page Source code
use_all_calibrations Man page Source code
use_calibrations Man page Source code
use_calibrations_bladj Man page Source code
use_calibrations_bladj.matchedCalibrations Man page Source code
use_calibrations_each Man page Source code
use_calibrations_pathd8 Man page Source code
use_calibrations_treePL Man page Source code
write.treePL Source code
phylotastic/datelife documentation built on Jan. 17, 2024, 11:10 p.m.

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