Scientific Data on Time of Lineage Divergence for Your Taxa
Get the Open Tree of Life Taxonomic identifier (OTT id) and name of al...
Figure out which subset function to use.
Get a taxon summary of a datelifeResult object.
Build grove list
Find the grove for a group of chronograms and build a matrix.
Check for conflicting calibrations.
Check input for usage in other datelife functions
Choose an ultrametric phylo object from cluster_patristicmatrix() ob...
Gets classification paths for a vector of taxa
Clean up some issues with Open Tree of Life chronograms For now it 1) ...
Identify, extract and clean taxonomic children names from a `taxonomy_...
Eliminates unmatched (NAs) and invalid taxa from a `rotl::tnrs_match_n...
Cluster a patristic matrix into a tree with various methods.
Congruify and Check.
Congruify nodes of a tree topology to nodes from a source chronogram, ...
Congruify nodes of a tree topology to nodes from a source chronogram, ...
Date with Paleobiology Database and paleotree.
Return the relevant authors for a set of studies.
Get a median summary chronogram from a datelifeResult object.
Compute a median matrix of a datelifeResult object.
Get a numeric vector of MRCAs from a datelifeResult object. Used in ...
Go from a datelifeResult object to a Super Distance Matrix (SDM) usi...
Reconstruct a supertree from a datelifeResult object using the Super...
Find the index of relevant studies in a cached chronogram database.
Compute a variance matrix of a datelifeResult object.
Get scientific, peer-reviewed information on time of lineage divergenc...
Generate one or multiple chronograms for a set of given taxon names.
Generate one or multiple chronograms for a set of taxon names given as...
Get the lineage of a set of taxa. .get_ott_lineage uses `rotl::taxon...
Use congruification to extract secondary calibrations from a `datelife...
Use congruification to extract secondary calibrations from a phylo o...
Extract numeric OTT ids from a character vector that combines taxon na...
Filter a datelifeResult object to find the largest grove.
Force a non-ultrametric phylo object to be ultrametric with `phytool...
Get secondary calibrations from a chronogram database for a set of giv...
Quickly get all species belonging to a taxon from the Open Tree of Lif...
Get grove from a datelifeResult object that can be converted to phyl...
Get the tree with the most tips from a multiPhylo object: the biggest ...
Get genetic data from the Barcode of Life Database (BOLD) for a set of...
Search and extract available secondary calibrations for taxon names in...
Search and extract secondary calibrations for a given character vector...
Get a dated OpenTree induced synthetic subtree from a set of given tax...
Get a patristic matrix of time of lineage divergence data for a given ...
Get a list of patristic matrices from a given datelifeQuery object
Get the ages for a taxon from PBDB
Get indices of good matrices to apply Super Distance Matrix (SDM) meth...
Makes a block of node constraints and node calibrations for a MrBayes ...
Get all chronograms from Open Tree of Life database
Get all species belonging to a taxon from the Open Tree of Life Taxono...
Get an Open Tree of Life synthetic subtree of a set of given taxon nam...
Use this instead of rotl::tol_subtree() when taxa are not in synthes...
Get the Open Tree of Life Taxonomic identifiers (OTT ids) and name of ...
Process a character vector of taxon names with TNRS
Extract valid children from given taxonomic name(s) or Open Tree of Li...
Process a phylo object or a character string to determine if it's corr...
Check if input is a datelifeQuery object
Check if we obtained an empty search with the given taxon name(s).
Check if a tree is a valid chronogram.
Function for computing n-overlap for two vectors of names (ie., phy1$t...
Find all authors and where they have deposited their trees
Use the BLADJ algorithm to get a chronogram from a tree topology for w...
Use genetic data from the Barcode of Life Database (BOLD) to reconstru...
Create a cache from Open Tree of Life
Go from taxon names to a datelifeQuery object
Go from taxon names to a datelifeQuery object
Make a mrBayes run block file with a constraint topology and a set of ...
Take a constraint tree and use mrBayes to get node ages and branch len...
Associate Open Tree of Life authors with studies
Create an overlap table
Make a Super Distance Matrix (SDM) from a list of good matrices obtain...
Associate TreeBase authors with studies
Create a cache from TreeBase
Add Open Tree of Life Taxonomy to tree nodes.
Match calibrations to nodes of a given tree
Go from a list of patristic distance matrix to a table of node ages
Go from a patristic distance matrix to a node ages table
Message for a multiPhylo input
Checks that missing_taxa argument is ok to be used by make_mrbayes_run...
Identify nodes of a tree topology that are most recent common ancestor...
patristic_matrix_array_congruify is used for patristic_matrix_array_...
Congruify a patristic matrix array from a given phylo object.
Split a patristic matrix array Used inside: patristic_matrix_array_con...
Subset a patristic matrix array
Are all desired taxa in the patristic matrix array?
Convert list of patristic matrices to a 3D array.
Get time of MRCA from patristic matrix. Used in `datelife_result_MRCA(...
Test the name order of a patristic matrix so that row and column label...
Reorder a matrix so that row and column labels are in alphabetical ord...
Fill in empty cells in a patristic matrix for missing taxa.
Are all desired taxa in the patristic matrix?
Convert patristic matrix to a newick string. Used inside: summarize_da...
Convert a patristic matrix to a phylo object.
Function to remove missing taxa from a datelifeResult object.
Checks if phy is a phylo object and/or a chronogram.
Congruify a reference tree and a target tree given as phylo objects.
Generate uncertainty in branch lengths using a lognormal.
Gets node numbers from any phylogeny
Get a subset array from a phylo object
Get a congruified subset array from a phylo object
Check if a tree has branch lengths
Prune missing taxa from a phylo object Used inside phylo_get_subset_...
Subset a reference and a target tree given as phylo objects.
Convert spaces to underscores in trees.
Convert underscores to spaces in trees.
Get a patristic matrix from a phylo object.
Pick a grove in the case of multiple groves in a set of trees.
Get an mrcaott tag from an OpenTree induced synthetic tree and get its...
Return the relevant curators for a set of studies.
Take results_list and process it.
Core function to generate results
Runs MrBayes from R
Sample trees from a file containing multiple trees. Usually from a bay...
Get summary statistics of ages in a congruifiedCalibrations object.
Summarize a datelifeResult object.
Summarize taxon age from PBDB to just a single min and max age
Gets all ages per taxon pair from a distance matrix Internal function ...
Summarize a datelifeResult object.
Summarize a matchedCalibrations object summary.matchedCalibrations...
Go from a summary matrix to an ultrametric phylo object.
Get minimum, median, mean, midpoint, and maximum summary chronograms f...
Summarize patristic matrix array (by default, median). Used inside: su...
Taxon name resolution service (tnrs) applied to a vector of names by b...
Add missing taxa to a dated tree and fabricate node ages for these mis...
Adds labels to nodes with no assigned label
Function to add an outgroup to any phylogeny, in phylo or newick forma...
Checks if a tree is a phylo class object otherwise it uses input_proce...
Take a tree with branch lengths and fix negative or zero length branch...
Gets a taxonomic tree from a vector of taxa
Get node numbers, node names, descendant tip numbers and labels of nod...
Identify the presence of a single lineage outgroup in a phylogeny
To get tip numbers descending from any given node of a tree
Update all data files as data objects for the package
Create an updated OpenTree chronograms database object
Date a given tree topology using a given set of congruified calibratio...
Date a given tree topology using a combined set of given calibrations
Use calibrations to date a topology with the BLADJ algorithm.
Use calibrations to date a topology with the BLADJ algorithm.
Date a given tree topology by using a given list of calibrations indep...
Date a tree with secondary calibrations using PATHd8
Date a tree with initial branch lengths with treePL.
Methods and workflows to get chronograms (i.e., phylogenetic trees with branch lengths proportional to time), using open, peer-reviewed, state-of-the-art scientific data on time of lineage divergence. This package constitutes the main underlying code of the DateLife web service at <https://www.datelife.org>. To obtain a single summary chronogram from a group of relevant chronograms, we implement the Super Distance Matrix (SDM) method described in Criscuolo et al. (2006) <doi:10.1080/10635150600969872>. To find the grove of chronograms with a sufficiently overlapping set of taxa for summarizing, we implement theorem 1.1. from Ané et al. (2009) <doi:10.1007/s00026-009-0017-x>. A given phylogenetic tree can be dated using time of lineage divergence data as secondary calibrations (with caution, see Schenk (2016) <doi:10.1371/journal.pone.0148228>). To obtain and apply secondary calibrations, the package implements the congruification method described in Eastman et al. (2013) <doi:10.1111/2041-210X.12051>. Tree dating can be performed with different methods including BLADJ (Webb et al. (2008) <doi:10.1093/bioinformatics/btn358>), PATHd8 (Britton et al. (2007) <doi:10.1080/10635150701613783>), mrBayes (Huelsenbeck and Ronquist (2001) <doi:10.1093/bioinformatics/17.8.754>), and treePL (Smith and O'Meara (2012) <doi:10.1093/bioinformatics/bts492>).