Man pages for phylotastic/datelife
Underlying Code for DateLife Web Service

batch_tnrs_match_namesTaxon name resolution service (tnrs) applied to input by...
birds_and_catsA multiPhylo object with trees resulting from a datelife...
build_grove_listBuild grove list
build_grove_matrixBuild grove matrix
clean_ott_chronogramClean up some issues with OToL chronograms
clean_tnrsEliminate unmatched (NAs) and invalid taxa from a...
contributor_cacheInformation on contributors, authors, study ids and clades...
datelife_authors_tabulateReturn the relevant authors for a set of studies
datelife_query_checkchecks if input is a datelifeQuery object, otherwise it uses...
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_medianFunction to compute median of a datelifeResult object.
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...
dlsearch_subset2A list with datelieQuery and datelifeResult objects from a...
felid_gdr_phylo_alldatelifeSummary of a datelifeResult object of all Felidae...
felid_sdmSDM tree of a datelifeResult object of all Felidae species.
filter_for_groveFilter a datelifeResult to find the largest grove
geostellarTable of geological ages and time before earth formation...
get_all_calibrationsGet all calibrations from chronograms in a database...
get_biggest_phyloGet the tree with the most tips: the biggest tree
get_dated_otol_induced_subtreeGet an otol induced dated subtree from your set of queried...
get_datelife_resultGo from a vector of species, newick string, or phylo object...
get_mrbayes_node_constraintsMakes a node constraints and node calibrations block for a...
get_otol_chronogramsGet all chronograms from Open Tree of Life
get_otol_synthetic_treeGets Open Tree of Life synthetic tree of a set of lineages.
get_subset_array_dispatchtry two types of NJ
input_processTakes a phylo object or a character string and figure out if...
is_good_chronogramCheck to see that a tree is a valid chronogram
is_n_overlapFunction for computing n overlap for two vectors of names...
make_all_associationsFind all authors and where they have deposited their trees
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_contributor_cacheCreate a cache from Open Tree of Life
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...
make_otol_associationsAssociate OToL authors with studies
make_overlap_tableCreate an overlap table
make_treebase_associationsAssociate TreeBase authors with studies
make_treebase_cacheCreate a cache from TreeBase
missing_taxa_checkChecks that missing_taxa argument is ok to be used by...
names_subset2Long list of >2.7k virus, bacteria, plant and animal taxon...
opentree_chronogramsChronograms in Open Tree of Life and other related data
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_generate_uncertaintyFunction to generate uncertainty in branch lengths using a...
phylo_get_node_numbersGets node numbers from any phylogeny
phylo_has_brlenCheck for branch lengths in a tree
phylo_height_omiget the outer margin of a graphics device from a number of...
phylo_tiplabel_space_to_underscoreConvert spaces to underscores in trees. Used in:...
phylo_tiplabel_underscore_to_spaceConvert underscores to spaces in trees. Used inside:...
pick_grovePick a grove in the case of multiple groves in a set of...
plant_bold_otol_treeSome plants chronogram
plot_densitreeget a densiTree plot from a set of opentree_chronograms if...
plot_phylo_allplot all trees with study titles and geochronological axis
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.
sample_treesFunction to sample trees from a file containing multiple...
save_otol_chronogramsSave all chronograms from Open Tree of Life
some_ants_datelife_resultdatelifeResult object of some ants
subset_treessubset trees for plotting densitree plots and phylo_all plots
summarize_datelife_resultSummarize a filtered results list from get_datelife_result...
summary_patristic_matrix_arraySummarize patristic matrix array (by default, median). Used...
tree_add_datesFabricates dates of missing taxa (with no data) on an already...
tree_add_nodelabelsAdds labels to nodes with no asigned label
tree_add_outgroupFunction to add an outgroup to any phylogeny, in phylo or...
treebase_cacheInformation on contributors, authors, study ids and clades...
tree_checkChecks if a tree is a phylo class object otherwise it uses...
tree_fix_brlenTakes a tree and fixes negative or zero length branches in...
tree_get_node_dataGets node numbers, node names, descendant tip numbers and...
tree_get_singleton_outgroupIdentifies the presence of a single lineage outgroup in a...
tree_node_tipsTo get tip numbers descending from any given node of a tree
update_all_cachedUpdate all cached files for the package
update_datelife_cacheupdate Open Tree of Life cache
use_all_calibrationsUse all calibrations from chronograms in a database to date a...
wrap_string_to_plotwrap a character string to a plotting area. It gives the...
phylotastic/datelife documentation built on Nov. 9, 2018, 12:11 p.m.