| birds_and_cats | A multiPhylo object with trees resulting from a datelife... |
| build_grove_list | Build grove list |
| build_grove_matrix | Find the grove for a group of chronograms and build a matrix. |
| check_conflicting_calibrations | Check for conflicting calibrations. |
| check_ott_input | Check input for usage in other 'datelife' functions |
| choose_cluster | Choose an ultrametric phylo object from... |
| classification_paths_from_taxonomy | Gets classification paths for a vector of taxa |
| clean_ott_chronogram | Clean up some issues with Open Tree of Life chronograms For... |
| clean_taxon_info_children | Identify, extract and clean taxonomic children names from a... |
| clean_tnrs | Eliminates unmatched (NAs) and invalid taxa from a... |
| cluster_patristicmatrix | Cluster a patristic matrix into a tree with various methods. |
| congruify_and_check | Congruify and Check. |
| congruify_and_mrca_multiPhylo | Congruify nodes of a tree topology to nodes from a source... |
| congruify_and_mrca_phylo | Congruify nodes of a tree topology to nodes from a source... |
| contributor_cache | Information on contributors, authors, study ids and clades... |
| datelife_authors_tabulate | Return the relevant authors for a set of studies. |
| datelife_result_median | Get a median summary chronogram from a 'datelifeResult'... |
| datelife_result_median_matrix | Compute a median matrix of a 'datelifeResult' object. |
| datelife_result_MRCA | Get a numeric vector of MRCAs from a 'datelifeResult' object.... |
| datelife_result_sdm_matrix | Go from a 'datelifeResult' object to a Super Distance Matrix... |
| datelife_result_sdm_phylo | Reconstruct a supertree from a 'datelifeResult' object using... |
| datelife_result_study_index | Find the index of relevant studies in a cached chronogram... |
| datelife_result_variance_matrix | Compute a variance matrix of a 'datelifeResult' object. |
| datelife_search | Get scientific, peer-reviewed information on time of lineage... |
| datelife_use | Generate one or multiple chronograms for a set of given taxon... |
| datelife_use_datelifequery | Generate one or multiple chronograms for a set of taxon names... |
| date_with_pbdb | Date with Paleobiology Database and paleotree. |
| dot-get_ott_lineage | Get the lineage of a set of taxa. '.get_ott_lineage' uses... |
| extract_calibrations_dateliferesult | Use congruification to extract secondary calibrations from a... |
| extract_calibrations_phylo | Use congruification to extract secondary calibrations from a... |
| extract_ott_ids | Extract numeric OTT ids from a character vector that combines... |
| felid_gdr_phylo_all | datelifeSummary of a datelifeResult object of all Felidae... |
| felid_sdm | SDM tree of a datelifeResult object of all Felidae species. |
| filter_for_grove | Filter a 'datelifeResult' object to find the largest grove. |
| force_ultrametric | Force a non-ultrametric 'phylo' object to be ultrametric with... |
| get_all_calibrations | Get secondary calibrations from a chronogram database for a... |
| get_all_descendant_species | Quickly get all species belonging to a taxon from the Open... |
| get_best_grove | Get grove from a 'datelifeResult' object that can be... |
| get_biggest_multiphylo | Get the tree with the most tips from a multiPhylo object: the... |
| get_bold_data | Get genetic data from the Barcode of Life Database (BOLD) for... |
| get_calibrations_datelifequery | Search and extract available secondary calibrations for taxon... |
| get_calibrations_vector | Search and extract secondary calibrations for a given... |
| get_dated_otol_induced_subtree | Get a dated OpenTree induced synthetic subtree from a set of... |
| get_datelife_result | Get a patristic matrix of time of lineage divergence data for... |
| get_datelife_result_datelifequery | Get a list of patristic matrices from a given 'datelifeQuery'... |
| get_fossil_range | Get the ages for a taxon from PBDB |
| get_goodmatrices | Get indices of good matrices to apply Super Distance Matrix... |
| get_mrbayes_node_constraints | Makes a block of node constraints and node calibrations for a... |
| get_opentree_chronograms | Get all chronograms from Open Tree of Life database |
| get_opentree_species | Get all species belonging to a taxon from the Open Tree of... |
| get_otol_synthetic_tree | Get an Open Tree of Life synthetic subtree of a set of given... |
| get_ott_children | Use this instead of 'rotl::tol_subtree()' when taxa are not... |
| get_ott_clade | Get the Open Tree of Life Taxonomic identifiers (OTT ids) and... |
| get_ott_lineage | Get the Open Tree of Life Taxonomic identifier (OTT id) and... |
| get_subset_array_dispatch | Figure out which subset function to use. |
| get_taxon_summary | Get a taxon summary of a 'datelifeResult' object. |
| get_tnrs_names | Process a character vector of taxon names with TNRS |
| get_valid_children | Extract valid children from given taxonomic name(s) or Open... |
| input_process | Process a phylo object or a character string to determine if... |
| is_datelife_query | Check if input is a 'datelifeQuery' object |
| is_datelife_result_empty | Check if we obtained an empty search with the given taxon... |
| is_good_chronogram | Check if a tree is a valid chronogram. |
| is_n_overlap | Function for computing n-overlap for two vectors of names... |
| make_all_associations | Find all authors and where they have deposited their trees |
| make_bladj_tree | Use the BLADJ algorithm to get a chronogram from a tree... |
| make_bold_otol_tree | Use genetic data from the Barcode of Life Database (BOLD) to... |
| make_contributor_cache | Create a cache from Open Tree of Life |
| make_datelife_query | Go from taxon names to a 'datelifeQuery' object |
| make_datelife_query2 | Go from taxon names to a 'datelifeQuery' object |
| make_mrbayes_runfile | Make a mrBayes run block file with a constraint topology and... |
| make_mrbayes_tree | Take a constraint tree and use mrBayes to get node ages and... |
| make_otol_associations | Associate Open Tree of Life authors with studies |
| make_overlap_table | Create an overlap table |
| make_sdm | Make a Super Distance Matrix (SDM) from a list of good... |
| make_treebase_associations | Associate TreeBase authors with studies |
| make_treebase_cache | Create a cache from TreeBase |
| map_nodes_ott | Add Open Tree of Life Taxonomy to tree nodes. |
| match_all_calibrations | Match calibrations to nodes of a given tree |
| matrices_to_table | Go from a list of patristic distance matrix to a table of... |
| matrix_to_table | Go from a patristic distance matrix to a node ages table |
| message_multiphylo | Message for a 'multiPhylo' input |
| missing_taxa_check | Checks that missing_taxa argument is ok to be used by... |
| mrca_calibrations | Identify nodes of a tree topology that are most recent common... |
| opentree_chronograms | Chronogram database |
| patristic_matrix_array_congruify | 'patristic_matrix_array_congruify' is used for... |
| patristic_matrix_array_phylo_congruify | Congruify a patristic matrix array from a given 'phylo'... |
| patristic_matrix_array_split | Split a patristic matrix array Used inside:... |
| patristic_matrix_array_subset | Subset a patristic matrix array |
| patristic_matrix_array_subset_both | Are all desired taxa in the patristic matrix array? |
| patristic_matrix_list_to_array | Convert list of patristic matrices to a 3D array. |
| patristic_matrix_MRCA | Get time of MRCA from patristic matrix. Used in... |
| patristic_matrix_name_order_test | Test the name order of a patristic matrix so that row and... |
| patristic_matrix_name_reorder | Reorder a matrix so that row and column labels are in... |
| patristic_matrix_pad | Fill in empty cells in a patristic matrix for missing taxa. |
| patristic_matrix_taxa_all_matching | Are all desired taxa in the patristic matrix? |
| patristic_matrix_to_newick | Convert patristic matrix to a newick string. Used inside:... |
| patristic_matrix_to_phylo | Convert a patristic matrix to a 'phylo' object. |
| patristic_matrix_unpad | Function to remove missing taxa from a 'datelifeResult'... |
| phylo_check | Checks if 'phy' is a 'phylo' object and/or a chronogram. |
| phylo_congruify | Congruify a reference tree and a target tree given as 'phylo'... |
| phylo_generate_uncertainty | Generate uncertainty in branch lengths using a lognormal. |
| phylo_get_node_numbers | Gets node numbers from any phylogeny |
| phylo_get_subset_array | Get a subset array from a 'phylo' object |
| phylo_get_subset_array_congruify | Get a congruified subset array from a 'phylo' object |
| phylo_has_brlen | Check if a tree has branch lengths |
| phylo_prune_missing_taxa | Prune missing taxa from a 'phylo' object Used inside... |
| phylo_subset_both | Subset a reference and a target tree given as 'phylo'... |
| phylo_tiplabel_space_to_underscore | Convert spaces to underscores in trees. |
| phylo_tiplabel_underscore_to_space | Convert underscores to spaces in trees. |
| phylo_to_patristic_matrix | Get a patristic matrix from a 'phylo' object. |
| pick_grove | Pick a grove in the case of multiple groves in a set of... |
| plant_bold_otol_tree | Some plants chronogram |
| problems | Problematic chronograms from Open Tree of Life. |
| recover_mrcaott | Get an mrcaott tag from an OpenTree induced synthetic tree... |
| relevant_curators_tabulate | Return the relevant curators for a set of studies. |
| results_list_process | Take results_list and process it. |
| run | Core function to generate results |
| run_mrbayes | Runs MrBayes from R |
| sample_trees | Sample trees from a file containing multiple trees. Usually... |
| some_ants_datelife_result | datelifeResult object of some ants |
| subset2_search | A list with datelifeQuery and datelifeResult objects from a... |
| subset2_taxa | Long list of >2.7k virus, bacteria, plant and animal taxon... |
| summarize_congruifiedCalibrations | Get summary statistics of ages in a 'congruifiedCalibrations'... |
| summarize_datelife_result | Summarize a 'datelifeResult' object. |
| summarize_fossil_range | Summarize taxon age from PBDB to just a single min and max... |
| summarize_summary_matrix | Gets all ages per taxon pair from a distance matrix Internal... |
| summary.datelifeResult | Summarize a 'datelifeResult' object. |
| summary.matchedCalibrations | Summarize a 'matchedCalibrations' object... |
| summary_matrix_to_phylo | Go from a summary matrix to an ultrametric 'phylo' object. |
| summary_matrix_to_phylo_all | Get minimum, median, mean, midpoint, and maximum summary... |
| summary_patristic_matrix_array | Summarize patristic matrix array (by default, median). Used... |
| threebirds_dr | 'datelifeResult' object of three birds "Rhea americana",... |
| tnrs_match | Taxon name resolution service (tnrs) applied to a vector of... |
| tree_add_dates | Add missing taxa to a dated tree and fabricate node ages for... |
| tree_add_nodelabels | Adds labels to nodes with no assigned label |
| tree_add_outgroup | Function to add an outgroup to any phylogeny, in phylo or... |
| treebase_cache | Information on contributors, authors, study ids and clades... |
| tree_check | Checks if a tree is a phylo class object otherwise it uses... |
| tree_fix_brlen | Take a tree with branch lengths and fix negative or zero... |
| tree_from_taxonomy | Gets a taxonomic tree from a vector of taxa |
| tree_get_node_data | Get node numbers, node names, descendant tip numbers and... |
| tree_get_singleton_outgroup | Identify the presence of a single lineage outgroup in a... |
| tree_node_tips | To get tip numbers descending from any given node of a tree |
| update_all_cached | Update all data files as data objects for the package |
| update_datelife_cache | Create an updated OpenTree chronograms database object |
| use_all_calibrations | Date a given tree topology using a given set of congruified... |
| use_calibrations | Date a given tree topology using a combined set of given... |
| use_calibrations_bladj | Use calibrations to date a topology with the BLADJ algorithm. |
| use_calibrations_bladj.matchedCalibrations | Use calibrations to date a topology with the BLADJ algorithm. |
| use_calibrations_each | Date a given tree topology by using a given list of... |
| use_calibrations_pathd8 | Date a tree with secondary calibrations using PATHd8 |
| use_calibrations_treePL | Date a tree with initial branch lengths with treePL. |
