.get_ott_lineage        Get the lineage of a set of taxa.
                        '.get_ott_lineage' uses
                        'rotl::taxonomy_taxon_info()' with
                        'include_lineage = TRUE'.
birds_and_cats          A multiPhylo object with trees resulting from a
                        datelife search of some birds and cats species
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
                        '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.
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 now it 1) checks unmapped taxa
                        and maps them with tnrs_match.phylo, 2) roots
                        the chronogram if unrooted
clean_taxon_info_children
                        Identify, extract and clean taxonomic children
                        names from a 'taxonomy_taxon_info()' output.
clean_tnrs              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.
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 chronogram, and find the mrca
                        nodes
congruify_and_mrca_phylo
                        Congruify nodes of a tree topology to nodes
                        from a source chronogram, and find the mrca
                        nodes
contributor_cache       Information on contributors, authors, study ids
                        and clades from studies with chronograms in
                        Open Tree of Life (Open Tree)
date_with_pbdb          Date with Paleobiology Database and paleotree.
datelife_authors_tabulate
                        Return the relevant authors for a set of
                        studies.
datelife_result_MRCA    Get a numeric vector of MRCAs from a
                        'datelifeResult' object. Used in
                        'summarize_datelife_result()'.
datelife_result_median
                        Get a median summary chronogram from a
                        'datelifeResult' object.
datelife_result_median_matrix
                        Compute a median matrix of a 'datelifeResult'
                        object.
datelife_result_sdm_matrix
                        Go from a 'datelifeResult' object to a Super
                        Distance Matrix (SDM) using weighting = "flat"
datelife_result_sdm_phylo
                        Reconstruct a supertree from a 'datelifeResult'
                        object using the Super Distance Matrix (SDM)
                        method.
datelife_result_study_index
                        Find the index of relevant studies in a cached
                        chronogram database.
datelife_result_variance_matrix
                        Compute a variance matrix of a 'datelifeResult'
                        object.
datelife_search         Get scientific, peer-reviewed information on
                        time of lineage divergence openly available for
                        a given set of taxon names
datelife_use            Generate one or multiple chronograms for a set
                        of given taxon names.
datelife_use_datelifequery
                        Generate one or multiple chronograms for a set
                        of taxon names given as a 'datelifeQuery'
                        object.
extract_calibrations_dateliferesult
                        Use congruification to extract secondary
                        calibrations from a 'datelifeResult' object.
extract_calibrations_phylo
                        Use congruification to extract secondary
                        calibrations from a 'phylo' or 'multiPhylo'
                        object with branch lengths proportional to
                        time.
extract_ott_ids         Extract numeric OTT ids from a character vector
                        that combines taxon names and OTT ids.
felid_gdr_phylo_all     datelifeSummary of a datelifeResult object of
                        all Felidae species.
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
                        'phytools::force.ultrametric()'.
get_all_calibrations    Get secondary calibrations from a chronogram
                        database for a set of given taxon names
get_best_grove          Get grove from a 'datelifeResult' object that
                        can be converted to phylo from a median summary
                        matrix
get_biggest_multiphylo
                        Get the tree with the most tips from a
                        multiPhylo object: the biggest tree.
get_bold_data           Get genetic data from the Barcode of Life
                        Database (BOLD) for a set of taxon names.
get_calibrations_datelifequery
                        Search and extract available secondary
                        calibrations for taxon names in a given
                        'datelifeQuery' object
get_calibrations_vector
                        Search and extract secondary calibrations for a
                        given character vector of taxon names
get_dated_otol_induced_subtree
                        Get a dated OpenTree induced synthetic subtree
                        from a set of given taxon names, from
                        blackrim's FePhyFoFum service.
get_datelife_result     Get a patristic matrix of time of lineage
                        divergence data for a given set of taxon names
get_datelife_result_datelifequery
                        Get a list of patristic matrices from a given
                        'datelifeQuery' object
get_fossil_range        Get the ages for a taxon from PBDB
get_goodmatrices        Get indices of good matrices to apply Super
                        Distance Matrix (SDM) method with 'make_sdm()'.
get_mrbayes_node_constraints
                        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_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 Life Taxonomy (OTT)
get_otol_synthetic_tree
                        Get an Open Tree of Life synthetic subtree of a
                        set of given taxon names.
get_ott_children        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_clade           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_lineage         Get the Open Tree of Life Taxonomic identifier
                        (OTT id) and name of all lineages from one or
                        more input taxa.
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 Tree of Life Taxonomic
                        identifiers (OTT ids) from a taxonomic source.
input_process           Process a phylo object or a character string to
                        determine if it's correct newick
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 name(s).
is_good_chronogram      Check if a tree is a valid chronogram.
is_n_overlap            Function for computing n-overlap for two
                        vectors of names (ie., phy1$tip.label,
                        phy2$tip.label) and seeing if they have n
                        overlap
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 topology for which you have age
                        data for some of its nodes.
make_bold_otol_tree     Use genetic data from the Barcode of Life
                        Database (BOLD) to reconstruct branch lengths
                        on a tree.
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 a set of node calibrations and
                        missing taxa
make_mrbayes_tree       Take a constraint tree and use mrBayes to get
                        node ages and branch lengths given a set of
                        node calibrations without any data.
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 matrices obtained with
                        'get_goodmatrices()'
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 node ages
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 make_mrbayes_runfile inside
                        tree_add_dates functions.
mrca_calibrations       Identify nodes of a tree topology that are most
                        recent common ancestor (mrca) of taxon pairs
                        from a 'calibrations' object
opentree_chronograms    Chronogram database
patristic_matrix_MRCA   Get time of MRCA from patristic matrix. Used in
                        'datelife_result_MRCA()'.
patristic_matrix_array_congruify
                        'patristic_matrix_array_congruify' is used for
                        patristic_matrix_array_subset_both and
                        patristic_matrix_array_congruify.
patristic_matrix_array_phylo_congruify
                        Congruify a patristic matrix array from a given
                        'phylo' object.
patristic_matrix_array_split
                        Split a patristic matrix array Used inside:
                        patristic_matrix_array_congruify
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_name_order_test
                        Test the name order of a patristic matrix so
                        that row and column labels are in alphabetical
                        order.
patristic_matrix_name_reorder
                        Reorder a matrix so that row and column labels
                        are in alphabetical order.
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: summarize_datelife_result.
patristic_matrix_to_phylo
                        Convert a patristic matrix to a 'phylo' object.
patristic_matrix_unpad
                        Function to remove missing taxa from a
                        'datelifeResult' object.
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' objects.
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_get_subset_array and
                        phylo_get_subset_array_congruify.
phylo_subset_both       Subset a reference and a target tree given as
                        'phylo' objects.
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 trees.
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 and get its name and ott id
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 from a bayesian analysis output
                        trees file.
some_ants_datelife_result
                        datelifeResult object of some ants
subset2_search          A list with datelifeQuery and datelifeResult
                        objects from a search of taxon names from
                        subset2_taxa
subset2_taxa            Long list of >2.7k virus, bacteria, plant and
                        animal taxon names
summarize_congruifiedCalibrations
                        Get summary statistics of ages in a
                        'congruifiedCalibrations' object.
summarize_datelife_result
                        Summarize a 'datelifeResult' object.
summarize_fossil_range
                        Summarize taxon age from PBDB to just a single
                        min and max age
summarize_summary_matrix
                        Gets all ages per taxon pair from a distance
                        matrix Internal function used in
                        summary_matrix_to_phylo_all().
summary.datelifeResult
                        Summarize a 'datelifeResult' object.
summary.matchedCalibrations
                        Summarize a 'matchedCalibrations' object
                        'summary.matchedCalibrations' gets the node age
                        distribution from 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 chronograms from a summary
                        matrix of a 'datelifeResult' object.
summary_patristic_matrix_array
                        Summarize patristic matrix array (by default,
                        median). Used inside:
                        summarize_datelife_result.
threebirds_dr           'datelifeResult' object of three birds "Rhea
                        americana", "Pterocnemia pennata", and
                        "Struthio camelus"
tnrs_match              Taxon name resolution service (tnrs) applied to
                        a vector of names by batches
tree_add_dates          Add missing taxa to a dated tree and fabricate
                        node ages for these missing taxa.
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 newick format
tree_check              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_fix_brlen          Take a tree with branch lengths and fix
                        negative or zero length branches.
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 labels of nodes from any tree, and
                        node ages from dated trees.
tree_get_singleton_outgroup
                        Identify the presence of a single lineage
                        outgroup in a phylogeny
tree_node_tips          To get tip numbers descending from any given
                        node of a tree
treebase_cache          Information on contributors, authors, study ids
                        and clades from studies with chronograms in
                        Open tree of Life
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 calibrations or ages
use_calibrations        Date a given tree topology using a combined set
                        of given calibrations
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 calibrations independently, to generate
                        multiple hypothesis of time of divergence
use_calibrations_pathd8
                        Date a tree with secondary calibrations using
                        PATHd8
use_calibrations_treePL
                        Date a tree with initial branch lengths with
                        treePL.
