# Scientific Data on Time of Lineage Divergence for Your Taxa

## Documentation for package ‘datelife’ version 0.6.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

B C D E F G I M O P R S T U misc

## -- B --

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.

## -- C --

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)

## -- D --

datelife | Get scientific, peer-reviewed information on time of lineage divergence openly available for a given set of taxon names
datelife_authors_tabulate | Return the relevant authors for a set of studies.
datelife_calibrations | Get secondary calibrations from a chronogram database for a set of given taxon names
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_MRCA | Get a numeric vector of MRCAs from a 'datelifeResult' object. Used in 'summarize_datelife_result()'.
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.
date_with_pbdb | Date with Paleobiology Database and paleotree.

## -- E --

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.
extract_ott_ids.default | Extract numeric OTT ids from a character vector that combines taxon names and OTT ids.

## -- F --

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()'.

## -- G --

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 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_chronograms | Get all chronograms from Open Tree of Life database
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.

## -- I --

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

## -- M --

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

## -- O --

opentree_chronograms | Chronogram database

## -- P --

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_MRCA | Get time of MRCA from patristic matrix. Used in 'datelife_result_MRCA()'.
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.

## -- R --

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

## -- S --

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.

## -- T --

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
tnrs_match.default | Taxon name resolution service (tnrs) applied to a vector of names by batches
tnrs_match.phylo | Taxon name resolution service (tnrs) applied to a vector of names by batches
treebase_cache | Information on contributors, authors, study ids and clades from studies with chronograms in Open tree of Life
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

## -- U --

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.

## -- misc --

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