Man pages for phylotastic/datelife
Underlying code for DateLife service

datelife_authors_tabulateReturn the relevant authors for a set of studies
datelife_query_length_checkchecks that we have at least two taxon names to perform a...
datelife_result_checkchecks if we obtained an empty search with the set of input...
datelife_result_MRCAGet vector of MRCAs from a datelifeResult object. Used in:...
datelife_result_sdmFunction to compute the SDM supertree (Criscuolo et al. 2006)...
datelife_result_study_indexFind the index of relevant studies in a opentree_chronograms...
datelife_searchCore function to input a vector of species, newick string, or...
get_all_calibrationsGet all calibrations from chronograms in a database...
get_datelife_resultGo from a vector of species, newick string, or phylo object...
get_mrbayes_node_calibrationsMakes a node calibrations block for a MrBayes run file from a...
get_subset_array_dispatchFigure out which subset function to use. Used inside:...
input_checkchecks if input has already been processed, otherwise it uses...
input_processTake input phylo object or character string and figure out if...
make_bladj_treeTakes a tree and uses bladj to estimate node ages and branch...
make_bold_otol_treeUse Barcode of Life data to get branch lengths on the OToL...
make_datelife_queryCleans taxon names from input character vector, phylo object...
make_mrbayes_runfileMakes a mrBayes run block file with a constraint topology and...
make_mrbayes_treeTakes a constraint tree and uses mrBayes to get node ages and...
missing_taxa_checkChecks that missing_taxa argument is ok to be used by...
opentree_chronogramsCached chronograms and other data from OpenTree
patristic_matrix_list_to_arrayConvert list of patristic matrices to a 3D array. Used...
patristic_matrix_MRCAGet time of MRCA from patristic matrix. Used in:...
patristic_matrix_name_reorderFunction to reorder a matrix so that row and column labels...
patristic_matrix_padFunction to fill in empty cells in a patristic matrix for...
patristic_matrix_taxa_all_matchingAre all desired taxa in the patristic_matrix? Used inside:...
patristic_matrix_to_newickConvert patristic matrix to a newick string. Used inside:...
patristic_matrix_to_phyloConvert patristic matrix to a phylo object. Used inside:...
patristic_matrix_unpadFunction to remove missing taxa from a datelifeResult object....
phylo_checkChecks if phy is a phylo class object and/or a chronogram
phylo_get_node_numbersGets node numbers from any phylogeny
phylo_tiplabel_space_to_underscoreConvert spaces to underscores in trees. Used in:...
phylo_tiplabel_underscore_to_spaceConvert underscores to spaces in trees. Used inside:...
relevant_curators_tabulateReturn the relevant curators for a set of studies
results_list_processTake results_list and process it. Used inside:...
runCore function to generate results
run_mrbayesRuns MrBayes from R.
summarize_datelife_resultSummarize a filtered results list from get_datelife_result...
summary_patristic_matrix_arraySummarize patristic matrix array (by default, median). Used...
update_datelife_cacheupdate Open Tree of Life cache
use_all_calibrationsUse all calibrations from chronograms in a database to date a...
phylotastic/datelife documentation built on Feb. 20, 2018, 7:21 p.m.