Function reference • datelife

All functions

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.

.get_ott_lineage(): Get the lineage of a set of taxa. .get_ott_lineage uses rotl::taxonomy_taxon_info() with include_lineage = TRUE.

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_all_calibrations(): Get secondary calibrations from a chronogram database for a set of given taxon names

get_all_descendant_species(): Quickly get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT)

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_otol_chronograms(): Get all chronograms from Open Tree of Life database using direct call from Open Tree API

get_opentree_chronograms_slow(): 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.