| Get the lineage of a set of taxa. '.get_ott_lineage' uses 'rotl::taxonomy_taxon_info()' with 'include_lineage = TRUE'. | .get_ott_lineage |
| A multiPhylo object with trees resulting from a datelife search of some birds and cats species | birds_and_cats |
| Build grove list | build_grove_list |
| Find the grove for a group of chronograms and build a matrix. | build_grove_matrix |
| Check for conflicting calibrations. | check_conflicting_calibrations |
| Check input for usage in other 'datelife' functions | check_ott_input |
| Choose an ultrametric phylo object from 'cluster_patristicmatrix()' obtained with a particular clustering method, or the next best tree. If there are no ultrametric trees, it does not force them to be ultrametric. | choose_cluster |
| Gets classification paths for a vector of taxa | classification_paths_from_taxonomy |
| Clean up some issues with Open Tree of Life chronograms For now it 1) checks unmapped taxa and maps them with tnrs_match.phylo, 2) roots the chronogram if unrooted | clean_ott_chronogram |
| Identify, extract and clean taxonomic children names from a 'taxonomy_taxon_info()' output. | clean_taxon_info_children |
| Eliminates unmatched (NAs) and invalid taxa from a 'rotl::tnrs_match_names()' or 'tnrs_match()' output Useful to get ott ids to retrieve an induced synthetic Open Tree of Life. Needed because using 'include_suppressed = FALSE' in 'rotl::tnrs_match_names()' does not drop all invalid taxa. | clean_tnrs |
| Cluster a patristic matrix into a tree with various methods. | cluster_patristicmatrix |
| Congruify and Check. | congruify_and_check |
| Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes | congruify_and_mrca_multiPhylo |
| Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes | congruify_and_mrca_phylo |
| Information on contributors, authors, study ids and clades from studies with chronograms in Open Tree of Life (Open Tree) | contributor_cache |
| Date with Paleobiology Database and paleotree. | date_with_pbdb |
| Return the relevant authors for a set of studies. | datelife_authors_tabulate |
| Get a median summary chronogram from a 'datelifeResult' object. | datelife_result_median |
| Compute a median matrix of a 'datelifeResult' object. | datelife_result_median_matrix |
| Get a numeric vector of MRCAs from a 'datelifeResult' object. Used in 'summarize_datelife_result()'. | datelife_result_MRCA |
| Go from a 'datelifeResult' object to a Super Distance Matrix (SDM) using weighting = "flat" | datelife_result_sdm_matrix |
| Reconstruct a supertree from a 'datelifeResult' object using the Super Distance Matrix (SDM) method. | datelife_result_sdm_phylo |
| Find the index of relevant studies in a cached chronogram database. | datelife_result_study_index |
| Compute a variance matrix of a 'datelifeResult' object. | datelife_result_variance_matrix |
| Get scientific, peer-reviewed information on time of lineage divergence openly available for a given set of taxon names | datelife datelife_search |
| Generate one or multiple chronograms for a set of given taxon names. | datelife_use |
| Generate one or multiple chronograms for a set of taxon names given as a 'datelifeQuery' object. | datelife_use_datelifequery |
| Use congruification to extract secondary calibrations from a 'datelifeResult' object. | extract_calibrations_dateliferesult |
| Use congruification to extract secondary calibrations from a 'phylo' or 'multiPhylo' object with branch lengths proportional to time. | extract_calibrations_phylo |
| Extract numeric OTT ids from a character vector that combines taxon names and OTT ids. | extract_ott_ids extract_ott_ids.default |
| datelifeSummary of a datelifeResult object of all Felidae species. | felid_gdr_phylo_all |
| SDM tree of a datelifeResult object of all Felidae species. | felid_sdm |
| Filter a 'datelifeResult' object to find the largest grove. | filter_for_grove |
| Force a non-ultrametric 'phylo' object to be ultrametric with 'phytools::force.ultrametric()'. | force_ultrametric |
| Get secondary calibrations from a chronogram database for a set of given taxon names | datelife_calibrations get_all_calibrations |
| Quickly get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT) | get_all_descendant_species |
| Get grove from a 'datelifeResult' object that can be converted to phylo from a median summary matrix | get_best_grove |
| Get the tree with the most tips from a multiPhylo object: the biggest tree. | get_biggest_multiphylo |
| Get genetic data from the Barcode of Life Database (BOLD) for a set of taxon names. | get_bold_data |
| Search and extract available secondary calibrations for taxon names in a given 'datelifeQuery' object | get_calibrations_datelifequery |
| Search and extract secondary calibrations for a given character vector of taxon names | get_calibrations_vector |
| Get a dated OpenTree induced synthetic subtree from a set of given taxon names, from blackrim's FePhyFoFum service. | get_dated_otol_induced_subtree |
| Get a patristic matrix of time of lineage divergence data for a given set of taxon names | get_datelife_result |
| Get a list of patristic matrices from a given 'datelifeQuery' object | get_datelife_result_datelifequery |
| Get the ages for a taxon from PBDB | get_fossil_range |
| Get indices of good matrices to apply Super Distance Matrix (SDM) method with 'make_sdm()'. | get_goodmatrices |
| Makes a block of node constraints and node calibrations for a MrBayes run file from a list of taxa and ages, or from a dated tree | get_mrbayes_node_constraints |
| Get all chronograms from Open Tree of Life database using direct call from Open Tree API | get_opentree_chronograms get_otol_chronograms |
| Get all chronograms from Open Tree of Life database | get_opentree_chronograms_slow |
| Get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT) | get_opentree_species |
| Get an Open Tree of Life synthetic subtree of a set of given taxon names. | get_otol_synthetic_tree |
| Use this instead of 'rotl::tol_subtree()' when taxa are not in synthesis tree and you still need to get all species or an induced OpenTree subtree | get_ott_children |
| Get the Open Tree of Life Taxonomic identifiers (OTT ids) and name of one or several given taxonomic ranks from one or more input taxa. | get_ott_clade |
| Get the Open Tree of Life Taxonomic identifier (OTT id) and name of all lineages from one or more input taxa. | get_ott_lineage |
| Figure out which subset function to use. | get_subset_array_dispatch |
| Get a taxon summary of a 'datelifeResult' object. | get_taxon_summary |
| Process a character vector of taxon names with TNRS | get_tnrs_names |
| Extract valid children from given taxonomic name(s) or Open Tree of Life Taxonomic identifiers (OTT ids) from a taxonomic source. | get_valid_children |
| Process a phylo object or a character string to determine if it's correct newick | input_process |
| Check if input is a 'datelifeQuery' object | is_datelife_query |
| Check if we obtained an empty search with the given taxon name(s). | is_datelife_result_empty |
| Check if a tree is a valid chronogram. | is_good_chronogram |
| Function for computing n-overlap for two vectors of names (ie., phy1$tip.label, phy2$tip.label) and seeing if they have n overlap | is_n_overlap |
| Find all authors and where they have deposited their trees | make_all_associations |
| Use the BLADJ algorithm to get a chronogram from a tree topology for which you have age data for some of its nodes. | make_bladj_tree |
| Use genetic data from the Barcode of Life Database (BOLD) to reconstruct branch lengths on a tree. | make_bold_otol_tree |
| Create a cache from Open Tree of Life | make_contributor_cache |
| Go from taxon names to a 'datelifeQuery' object | make_datelife_query |
| Go from taxon names to a 'datelifeQuery' object | make_datelife_query2 |
| Make a mrBayes run block file with a constraint topology and a set of node calibrations and missing taxa | make_mrbayes_runfile |
| Take a constraint tree and use mrBayes to get node ages and branch lengths given a set of node calibrations without any data. | make_mrbayes_tree |
| Associate Open Tree of Life authors with studies | make_otol_associations |
| Create an overlap table | make_overlap_table |
| Make a Super Distance Matrix (SDM) from a list of good matrices obtained with 'get_goodmatrices()' | make_sdm |
| Associate TreeBase authors with studies | make_treebase_associations |
| Create a cache from TreeBase | make_treebase_cache |
| Add Open Tree of Life Taxonomy to tree nodes. | map_nodes_ott |
| Match calibrations to nodes of a given tree | match_all_calibrations |
| Go from a list of patristic distance matrix to a table of node ages | matrices_to_table |
| Go from a patristic distance matrix to a node ages table | matrix_to_table |
| Message for a 'multiPhylo' input | message_multiphylo |
| Checks that missing_taxa argument is ok to be used by make_mrbayes_runfile inside tree_add_dates functions. | missing_taxa_check |
| Identify nodes of a tree topology that are most recent common ancestor (mrca) of taxon pairs from a 'calibrations' object | mrca_calibrations |
| Chronogram database | opentree_chronograms |
| 'patristic_matrix_array_congruify' is used for patristic_matrix_array_subset_both and patristic_matrix_array_congruify. | patristic_matrix_array_congruify |
| Congruify a patristic matrix array from a given 'phylo' object. | patristic_matrix_array_phylo_congruify |
| Split a patristic matrix array Used inside: patristic_matrix_array_congruify | patristic_matrix_array_split |
| Subset a patristic matrix array | patristic_matrix_array_subset |
| Are all desired taxa in the patristic matrix array? | patristic_matrix_array_subset_both |
| Convert list of patristic matrices to a 3D array. | patristic_matrix_list_to_array |
| Get time of MRCA from patristic matrix. Used in 'datelife_result_MRCA()'. | patristic_matrix_MRCA |
| Test the name order of a patristic matrix so that row and column labels are in alphabetical order. | patristic_matrix_name_order_test |
| Reorder a matrix so that row and column labels are in alphabetical order. | patristic_matrix_name_reorder |
| Fill in empty cells in a patristic matrix for missing taxa. | patristic_matrix_pad |
| Are all desired taxa in the patristic matrix? | patristic_matrix_taxa_all_matching |
| Convert patristic matrix to a newick string. Used inside: summarize_datelife_result. | patristic_matrix_to_newick |
| Convert a patristic matrix to a 'phylo' object. | patristic_matrix_to_phylo |
| Function to remove missing taxa from a 'datelifeResult' object. | patristic_matrix_unpad |
| Checks if 'phy' is a 'phylo' object and/or a chronogram. | phylo_check |
| Congruify a reference tree and a target tree given as 'phylo' objects. | phylo_congruify |
| Generate uncertainty in branch lengths using a lognormal. | phylo_generate_uncertainty |
| Gets node numbers from any phylogeny | phylo_get_node_numbers |
| Get a subset array from a 'phylo' object | phylo_get_subset_array |
| Get a congruified subset array from a 'phylo' object | phylo_get_subset_array_congruify |
| Check if a tree has branch lengths | phylo_has_brlen |
| Prune missing taxa from a 'phylo' object Used inside phylo_get_subset_array and phylo_get_subset_array_congruify. | phylo_prune_missing_taxa |
| Subset a reference and a target tree given as 'phylo' objects. | phylo_subset_both |
| Convert spaces to underscores in trees. | phylo_tiplabel_space_to_underscore |
| Convert underscores to spaces in trees. | phylo_tiplabel_underscore_to_space |
| Get a patristic matrix from a 'phylo' object. | phylo_to_patristic_matrix |
| Pick a grove in the case of multiple groves in a set of trees. | pick_grove |
| Some plants chronogram | plant_bold_otol_tree |
| Problematic chronograms from Open Tree of Life. | problems |
| Get an mrcaott tag from an OpenTree induced synthetic tree and get its name and ott id | recover_mrcaott |
| Return the relevant curators for a set of studies. | relevant_curators_tabulate |
| Take results_list and process it. | results_list_process |
| Core function to generate results | run |
| Runs MrBayes from R | run_mrbayes |
| Sample trees from a file containing multiple trees. Usually from a bayesian analysis output trees file. | sample_trees |
| datelifeResult object of some ants | some_ants_datelife_result |
| A list with datelifeQuery and datelifeResult objects from a search of taxon names from subset2_taxa | subset2_search |
| Long list of >2.7k virus, bacteria, plant and animal taxon names | subset2_taxa |
| Get summary statistics of ages in a 'congruifiedCalibrations' object. | summarize_congruifiedCalibrations |
| Summarize a 'datelifeResult' object. | summarize_datelife_result |
| Summarize taxon age from PBDB to just a single min and max age | summarize_fossil_range |
| Gets all ages per taxon pair from a distance matrix Internal function used in summary_matrix_to_phylo_all(). | summarize_summary_matrix |
| Go from a summary matrix to an ultrametric 'phylo' object. | summary_matrix_to_phylo |
| Get minimum, median, mean, midpoint, and maximum summary chronograms from a summary matrix of a 'datelifeResult' object. | summary_matrix_to_phylo_all |
| Summarize patristic matrix array (by default, median). Used inside: summarize_datelife_result. | summary_patristic_matrix_array |
| Summarize a 'datelifeResult' object. | summary.datelifeResult |
| Summarize a 'matchedCalibrations' object 'summary.matchedCalibrations' gets the node age distribution from a 'matchedCalibrations' object. | summary.matchedCalibrations |
| 'datelifeResult' object of three birds "Rhea americana", "Pterocnemia pennata", and "Struthio camelus" | threebirds_dr |
| Taxon name resolution service (tnrs) applied to a vector of names by batches | tnrs_match tnrs_match.default tnrs_match.phylo |
| Add missing taxa to a dated tree and fabricate node ages for these missing taxa. | tree_add_dates |
| Adds labels to nodes with no assigned label | tree_add_nodelabels |
| Function to add an outgroup to any phylogeny, in phylo or newick format | tree_add_outgroup |
| Checks if a tree is a phylo class object otherwise it uses input_process. Additionally it can check if tree is a chronogram with phylo_check | tree_check |
| Take a tree with branch lengths and fix negative or zero length branches. | tree_fix_brlen |
| Gets a taxonomic tree from a vector of taxa | tree_from_taxonomy |
| Get node numbers, node names, descendant tip numbers and labels of nodes from any tree, and node ages from dated trees. | tree_get_node_data |
| Identify the presence of a single lineage outgroup in a phylogeny | tree_get_singleton_outgroup |
| To get tip numbers descending from any given node of a tree | tree_node_tips |
| Information on contributors, authors, study ids and clades from studies with chronograms in Open tree of Life | treebase_cache |
| Update all data files as data objects for the package | update_all_cached |
| Create an updated OpenTree chronograms database object | update_datelife_cache |
| Date a given tree topology using a given set of congruified calibrations or ages | use_all_calibrations |
| Date a given tree topology using a combined set of given calibrations | use_calibrations |
| Use calibrations to date a topology with the BLADJ algorithm. | use_calibrations_bladj |
| Use calibrations to date a topology with the BLADJ algorithm. | use_calibrations_bladj.matchedCalibrations |
| Date a given tree topology by using a given list of calibrations independently, to generate multiple hypothesis of time of divergence | use_calibrations_each |
| Date a tree with secondary calibrations using PATHd8 | use_calibrations_pathd8 |
| Date a tree with initial branch lengths with treePL. | use_calibrations_treePL |
