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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
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.