{ "_id": "6a1f2af7b401979e73424f23", "Package": "datelife", "Title": "Scientific Data on Time of Lineage Divergence for Your Taxa", "Version": "0.6.9", "Maintainer": "Luna L. Sanchez Reyes ", "Authors@R": "c(\nperson(\"Brian\", \"O'Meara\", email = \"bomeara@gmail.com\", role=c(\"aut\")),\nperson(\"Jonathan\", \"Eastman\", role=c(\"aut\")),\nperson(\"Tracy\", \"Heath\", role=c(\"aut\")),\nperson(\"April\", \"Wright\", role=c(\"aut\")),\nperson(\"Klaus\", \"Schliep\", role=c(\"aut\")),\nperson(\"Scott\", \"Chamberlain\", role=c(\"aut\")),\nperson(\"Peter\", \"Midford\", role=c(\"aut\")),\nperson(\"Luke\", \"Harmon\", role=c(\"aut\")),\nperson(\"Joseph\", \"Brown\", role=c(\"aut\")),\nperson(\"Matt\", \"Pennell\", role=c(\"aut\")),\nperson(\"Mike\", \"Alfaro\", role=c(\"aut\")),\nperson(\"Luna L.\", \"Sanchez Reyes\", email = \"sanchez.reyes.luna@gmail.com\", role=c(\"aut\", \"cre\")),\nperson(\"Emily Jane\", \"McTavish\", role=c(\"ctb\")))", "Description": "Methods and workflows to get chronograms (i.e.,\nphylogenetic trees with branch lengths proportional to time),\nusing open, peer-reviewed, state-of-the-art scientific data on\ntime of lineage divergence. This package constitutes the main\nunderlying code of the DateLife web service at\n. To obtain a single summary\nchronogram from a group of relevant chronograms, we implement\nthe Super Distance Matrix (SDM) method described in Criscuolo\net al. (2006) . To find the\ngrove of chronograms with a sufficiently overlapping set of\ntaxa for summarizing, we implement theorem 1.1. from Ané et al.\n(2009) . A given phylogenetic\ntree can be dated using time of lineage divergence data as\nsecondary calibrations (with caution, see Schenk (2016)\n). To obtain and apply\nsecondary calibrations, the package implements the\ncongruification method described in Eastman et al. (2013)\n. Tree dating can be performed\nwith different methods including BLADJ (Webb et al. (2008)\n), PATHd8 (Britton et al.\n(2007) ), mrBayes (Huelsenbeck\nand Ronquist (2001) ), and\ntreePL (Smith and O'Meara (2012)\n).", "biocViews": "Software", "LazyDataCompression": "xz", "SystemRequirements": "PATHd8", "URL": "https://github.com/phylotastic/datelife,\nhttp://phylotastic.org/datelife/", "License": "GPL (>=2)", "LazyData": "true", "RoxygenNote": "7.2.3", "Roxygen": "list(markdown = TRUE)", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Language": "en-US", "Config/pak/sysreqs": "libglpk-dev make libicu-dev libpng-dev libxml2-dev\nlibssl-dev", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2025-11-02 17:40:04 UTC", "RemoteUrl": "https://github.com/phylotastic/datelife", "RemoteRef": "HEAD", "RemoteSha": "e1ff3e41f4e41ad79b060cdfc974dd893eee9ff3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 19:05:25 UTC", "User": "root" }, "Author": "Brian O'Meara [aut],\nJonathan Eastman [aut],\nTracy Heath [aut],\nApril Wright [aut],\nKlaus Schliep [aut],\nScott Chamberlain [aut],\nPeter Midford [aut],\nLuke Harmon [aut],\nJoseph Brown [aut],\nMatt Pennell [aut],\nMike Alfaro [aut],\nLuna L. Sanchez Reyes [aut, cre],\nEmily Jane McTavish [ctb]", "MD5sum": "bd33e8d30a0e656411f52046e17429f8", "_user": "phylotastic", "_type": "src", "_file": "datelife_0.6.9.tar.gz", "_fileid": "0a2e72dc4a1d406bec871d58763b497d5c982d27d4c782fb75969efd9b3321c8", "_filesize": 8190921, "_sha256": "0a2e72dc4a1d406bec871d58763b497d5c982d27d4c782fb75969efd9b3321c8", "_created": "2026-06-02T19:05:25.000Z", "_published": "2026-06-02T19:11:51.711Z", "_distro": "noble", "_jobs": [ { "job": 79150801801, "time": 200, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7367351042" }, { "job": 79150801858, "time": 197, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7367350159" }, { "job": 79150801739, "time": 152, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7367399520" }, { "job": 79150801873, "time": 123, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7367389748" }, { "job": 79149593393, "time": 384, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7367278153" }, { "job": 79150801788, "time": 170, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7367340513" }, { "job": 79150801832, "time": 134, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7367327301" }, { "job": 79150802011, "time": 111, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7367319266" }, { "job": 79150801846, "time": 181, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7367344707" } ], "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841490491", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/phylotastic/datelife", "_commit": { "id": "e1ff3e41f4e41ad79b060cdfc974dd893eee9ff3", "author": "Brian O'Meara ", "committer": "Brian O'Meara ", "message": "updated object name\n", "time": 1762105204 }, "_maintainer": { "name": "Luna L. Sanchez Reyes", "email": "sanchez.reyes.luna@gmail.com", "login": "lunasare", "twitter": "@LunaSare", "description": "Nature. Computers. 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"version": "0.6.0", "date": "2022-01-17" }, { "version": "0.6.1", "date": "2022-01-31" }, { "version": "0.6.5", "date": "2022-06-21" }, { "version": "0.6.6", "date": "2022-12-16" }, { "version": "0.6.7", "date": "2023-05-09" }, { "version": "0.6.8", "date": "2023-06-20" } ], "_exports": [ "build_grove_list", "build_grove_matrix", "check_ott_input", "choose_cluster", "classification_paths_from_taxonomy", "clean_ott_chronogram", "clean_taxon_info_children", "clean_tnrs", "cluster_patristicmatrix", "congruify_and_mrca_multiPhylo", "congruify_and_mrca_phylo", "date_with_pbdb", "datelife_authors_tabulate", "datelife_result_median", "datelife_result_median_matrix", "datelife_result_sdm_matrix", "datelife_result_sdm_phylo", "datelife_result_variance_matrix", "datelife_search", "datelife_use", "datelife_use_datelifequery", "extract_calibrations_dateliferesult", "extract_calibrations_phylo", "extract_ott_ids", "filter_for_grove", "force_ultrametric", "get_all_calibrations", "get_all_descendant_species", "get_best_grove", "get_biggest_multiphylo", "get_bold_data", "get_calibrations_datelifequery", "get_calibrations_vector", "get_dated_otol_induced_subtree", "get_datelife_result", "get_datelife_result_datelifequery", "get_fossil_range", "get_goodmatrices", "get_mrbayes_node_constraints", "get_opentree_chronograms", "get_opentree_species", "get_otol_chronograms", "get_otol_synthetic_tree", "get_ott_children", "get_ott_clade", "get_ott_lineage", "get_taxon_summary", "get_tnrs_names", "get_valid_children", "input_process", "is_datelife_query", "is_datelife_result_empty", "is_good_chronogram", "is_n_overlap", "make_bladj_tree", "make_bold_otol_tree", "make_contributor_cache", "make_datelife_query", "make_datelife_query2", "make_mrbayes_runfile", "make_mrbayes_tree", "make_overlap_table", "make_sdm", "make_treebase_cache", "map_nodes_ott", "matrices_to_table", "matrix_to_table", "missing_taxa_check", "mrca_calibrations", "patristic_matrix_to_newick", 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"multiPhylo" ], "fields": [], "table": true, "tojson": false }, { "name": "contributor_cache", "title": "Information on contributors, authors, study ids and clades from studies with chronograms in Open Tree of Life (Open Tree)", "object": "contributor_cache", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "felid_gdr_phylo_all", "title": "datelifeSummary of a datelifeResult object of all Felidae species.", "object": "felid_gdr_phylo_all", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "felid_sdm", "title": "SDM tree of a datelifeResult object of all Felidae species.", "object": "felid_sdm", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "opentree_chronograms", "title": "Chronogram database", "object": "opentree_chronograms", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "plant_bold_otol_tree", "title": "Some plants chronogram", "object": "plant_bold_otol_tree", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "problems", "title": "Problematic chronograms from Open Tree of Life.", "object": "problems", "class": [ "list" ], "fields": [], "table": true, "tojson": false }, { "name": "some_ants_datelife_result", "title": "datelifeResult object of some ants", "object": "some_ants_datelife_result", "class": [ "datelifeResult" ], "fields": [], "table": true, "tojson": false }, { "name": "subset2_search", "title": "A list with datelifeQuery and datelifeResult objects from a search of taxon names from subset2_taxa", "object": "subset2_search", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "subset2_taxa", "title": "Long list of >2.7k virus, bacteria, plant and animal taxon names", "object": "subset2_taxa", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "threebirds_dr", "title": "'datelifeResult' object of three birds \"Rhea americana\", \"Pterocnemia pennata\", and \"Struthio camelus\"", "object": "threebirds_dr", "class": [ "datelifeResult" ], "fields": [], "table": false, "tojson": false }, { "name": "treebase_cache", "title": "Information on contributors, authors, study ids and clades from studies with chronograms in Open tree of Life", "object": "treebase_cache", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "dot-get_ott_lineage", "title": "Get the lineage of a set of taxa. '.get_ott_lineage' uses 'rotl::taxonomy_taxon_info()' with 'include_lineage = TRUE'.", "topics": [ ".get_ott_lineage" ] }, { "page": "birds_and_cats", "title": "A multiPhylo object with trees resulting from a datelife search of some birds and cats species", "topics": [ "birds_and_cats" ] }, { "page": "build_grove_list", "title": "Build grove list", "topics": [ "build_grove_list" ] }, { "page": "build_grove_matrix", "title": "Find the grove for a group of chronograms and build a matrix.", "topics": [ "build_grove_matrix" ] }, { "page": "check_conflicting_calibrations", "title": "Check for conflicting calibrations.", "topics": [ "check_conflicting_calibrations" ] }, { "page": "check_ott_input", "title": "Check input for usage in other 'datelife' functions", "topics": [ "check_ott_input" ] }, { "page": "choose_cluster", "title": "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.", "topics": [ "choose_cluster" ] }, { "page": "classification_paths_from_taxonomy", "title": "Gets classification paths for a vector of taxa", "topics": [ "classification_paths_from_taxonomy" ] }, { "page": "clean_ott_chronogram", "title": "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", "topics": [ "clean_ott_chronogram" ] }, { "page": "clean_taxon_info_children", "title": "Identify, extract and clean taxonomic children names from a 'taxonomy_taxon_info()' output.", "topics": [ "clean_taxon_info_children" ] }, { "page": "clean_tnrs", "title": "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.", "topics": [ "clean_tnrs" ] }, { "page": "cluster_patristicmatrix", "title": "Cluster a patristic matrix into a tree with various methods.", "topics": [ "cluster_patristicmatrix" ] }, { "page": "congruify_and_check", "title": "Congruify and Check.", "topics": [ "congruify_and_check" ] }, { "page": "congruify_and_mrca_multiPhylo", "title": "Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes", "topics": [ "congruify_and_mrca_multiPhylo" ] }, { "page": "congruify_and_mrca_phylo", "title": "Congruify nodes of a tree topology to nodes from a source chronogram, and find the mrca nodes", "topics": [ "congruify_and_mrca_phylo" ] }, { "page": "contributor_cache", "title": "Information on contributors, authors, study ids and clades from studies with chronograms in Open Tree of Life (Open Tree)", "topics": [ "contributor_cache" ] }, { "page": "date_with_pbdb", "title": "Date with Paleobiology Database and paleotree.", "topics": [ "date_with_pbdb" ] }, { "page": "datelife_authors_tabulate", "title": "Return the relevant authors for a set of studies.", "topics": [ "datelife_authors_tabulate" ] }, { "page": "datelife_result_median", "title": "Get a median summary chronogram from a 'datelifeResult' object.", "topics": [ "datelife_result_median" ] }, { "page": "datelife_result_median_matrix", "title": "Compute a median matrix of a 'datelifeResult' object.", "topics": [ "datelife_result_median_matrix" ] }, { "page": "datelife_result_MRCA", "title": "Get a numeric vector of MRCAs from a 'datelifeResult' object. Used in 'summarize_datelife_result()'.", "topics": [ "datelife_result_MRCA" ] }, { "page": "datelife_result_sdm_matrix", "title": "Go from a 'datelifeResult' object to a Super Distance Matrix (SDM) using weighting = \"flat\"", "topics": [ "datelife_result_sdm_matrix" ] }, { "page": "datelife_result_sdm_phylo", "title": "Reconstruct a supertree from a 'datelifeResult' object using the Super Distance Matrix (SDM) method.", "topics": [ "datelife_result_sdm_phylo" ] }, { "page": "datelife_result_study_index", "title": "Find the index of relevant studies in a cached chronogram database.", "topics": [ "datelife_result_study_index" ] }, { "page": "datelife_result_variance_matrix", "title": "Compute a variance matrix of a 'datelifeResult' object.", "topics": [ "datelife_result_variance_matrix" ] }, { "page": "datelife_search", "title": "Get scientific, peer-reviewed information on time of lineage divergence openly available for a given set of taxon names", "topics": [ "datelife", "datelife_search" ] }, { "page": "datelife_use", "title": "Generate one or multiple chronograms for a set of given taxon names.", "topics": [ "datelife_use" ] }, { "page": "datelife_use_datelifequery", "title": "Generate one or multiple chronograms for a set of taxon names given as a 'datelifeQuery' object.", "topics": [ "datelife_use_datelifequery" ] }, { "page": "extract_calibrations_dateliferesult", "title": "Use congruification to extract secondary calibrations from a 'datelifeResult' object.", "topics": [ "extract_calibrations_dateliferesult" ] }, { "page": "extract_calibrations_phylo", "title": "Use congruification to extract secondary calibrations from a 'phylo' or 'multiPhylo' object with branch lengths proportional to time.", "topics": [ "extract_calibrations_phylo" ] }, { "page": "extract_ott_ids", "title": "Extract numeric OTT ids from a character vector that combines taxon names and OTT ids.", "topics": [ "extract_ott_ids", "extract_ott_ids.default" ] }, { "page": "felid_gdr_phylo_all", "title": "datelifeSummary of a datelifeResult object of all Felidae species.", "topics": [ "felid_gdr_phylo_all" ] }, { "page": "felid_sdm", "title": "SDM tree of a datelifeResult object of all Felidae species.", "topics": [ "felid_sdm" ] }, { "page": "filter_for_grove", "title": "Filter a 'datelifeResult' object to find the largest grove.", "topics": [ "filter_for_grove" ] }, { "page": "force_ultrametric", "title": "Force a non-ultrametric 'phylo' object to be ultrametric with 'phytools::force.ultrametric()'.", "topics": [ "force_ultrametric" ] }, { "page": "get_all_calibrations", "title": "Get secondary calibrations from a chronogram database for a set of given taxon names", "topics": [ "datelife_calibrations", "get_all_calibrations" ] }, { "page": "get_all_descendant_species", "title": "Quickly get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT)", "topics": [ "get_all_descendant_species" ] }, { "page": "get_best_grove", "title": "Get grove from a 'datelifeResult' object that can be converted to phylo from a median summary matrix", "topics": [ "get_best_grove" ] }, { "page": "get_biggest_multiphylo", "title": "Get the tree with the most tips from a multiPhylo object: the biggest tree.", "topics": [ "get_biggest_multiphylo" ] }, { "page": "get_bold_data", "title": "Get genetic data from the Barcode of Life Database (BOLD) for a set of taxon names.", "topics": [ "get_bold_data" ] }, { "page": "get_calibrations_datelifequery", "title": "Search and extract available secondary calibrations for taxon names in a given 'datelifeQuery' object", "topics": [ "get_calibrations_datelifequery" ] }, { "page": "get_calibrations_vector", "title": "Search and extract secondary calibrations for a given character vector of taxon names", "topics": [ "get_calibrations_vector" ] }, { "page": "get_dated_otol_induced_subtree", "title": "Get a dated OpenTree induced synthetic subtree from a set of given taxon names, from blackrim's FePhyFoFum service.", "topics": [ "get_dated_otol_induced_subtree" ] }, { "page": "get_datelife_result", "title": "Get a patristic matrix of time of lineage divergence data for a given set of taxon names", "topics": [ "get_datelife_result" ] }, { "page": "get_datelife_result_datelifequery", "title": "Get a list of patristic matrices from a given 'datelifeQuery' object", "topics": [ "get_datelife_result_datelifequery" ] }, { "page": "get_fossil_range", "title": "Get the ages for a taxon from PBDB", "topics": [ "get_fossil_range" ] }, { "page": "get_goodmatrices", "title": "Get indices of good matrices to apply Super Distance Matrix (SDM) method with 'make_sdm()'.", "topics": [ "get_goodmatrices" ] }, { "page": "get_mrbayes_node_constraints", "title": "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", "topics": [ "get_mrbayes_node_constraints" ] }, { "page": "get_opentree_chronograms", "title": "Get all chronograms from Open Tree of Life database using direct call from Open Tree API", "topics": [ "get_opentree_chronograms", "get_otol_chronograms" ] }, { "page": "get_opentree_chronograms_slow", "title": "Get all chronograms from Open Tree of Life database", "topics": [ "get_opentree_chronograms_slow" ] }, { "page": "get_opentree_species", "title": "Get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT)", "topics": [ "get_opentree_species" ] }, { "page": "get_otol_synthetic_tree", "title": "Get an Open Tree of Life synthetic subtree of a set of given taxon names.", "topics": [ "get_otol_synthetic_tree" ] }, { "page": "get_ott_children", "title": "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", "topics": [ "get_ott_children" ] }, { "page": "get_ott_clade", "title": "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.", "topics": [ "get_ott_clade" ] }, { "page": "get_ott_lineage", "title": "Get the Open Tree of Life Taxonomic identifier (OTT id) and name of all lineages from one or more input taxa.", "topics": [ "get_ott_lineage" ] }, { "page": "get_subset_array_dispatch", "title": "Figure out which subset function to use.", "topics": [ "get_subset_array_dispatch" ] }, { "page": "get_taxon_summary", "title": "Get a taxon summary of a 'datelifeResult' object.", "topics": [ "get_taxon_summary" ] }, { "page": "get_tnrs_names", "title": "Process a character vector of taxon names with TNRS", "topics": [ "get_tnrs_names" ] }, { "page": "get_valid_children", "title": "Extract valid children from given taxonomic name(s) or Open Tree of Life Taxonomic identifiers (OTT ids) from a taxonomic source.", "topics": [ "get_valid_children" ] }, { "page": "input_process", "title": "Process a phylo object or a character string to determine if it's correct newick", "topics": [ "input_process" ] }, { "page": "is_datelife_query", "title": "Check if input is a 'datelifeQuery' object", "topics": [ "is_datelife_query" ] }, { "page": "is_datelife_result_empty", "title": "Check if we obtained an empty search with the given taxon name(s).", "topics": [ "is_datelife_result_empty" ] }, { "page": "is_good_chronogram", "title": "Check if a tree is a valid chronogram.", "topics": [ "is_good_chronogram" ] }, { "page": "is_n_overlap", "title": "Function for computing n-overlap for two vectors of names (ie., phy1$tip.label, phy2$tip.label) and seeing if they have n overlap", "topics": [ "is_n_overlap" ] }, { "page": "make_all_associations", "title": "Find all authors and where they have deposited their trees", "topics": [ "make_all_associations" ] }, { "page": "make_bladj_tree", "title": "Use the BLADJ algorithm to get a chronogram from a tree topology for which you have age data for some of its nodes.", "topics": [ "make_bladj_tree" ] }, { "page": "make_bold_otol_tree", "title": "Use genetic data from the Barcode of Life Database (BOLD) to reconstruct branch lengths on a tree.", "topics": [ "make_bold_otol_tree" ] }, { "page": "make_contributor_cache", "title": "Create a cache from Open Tree of Life", "topics": [ "make_contributor_cache" ] }, { "page": "make_datelife_query", "title": "Go from taxon names to a 'datelifeQuery' object", "topics": [ "make_datelife_query" ] }, { "page": "make_datelife_query2", "title": "Go from taxon names to a 'datelifeQuery' object", "topics": [ "make_datelife_query2" ] }, { "page": "make_mrbayes_runfile", "title": "Make a mrBayes run block file with a constraint topology and a set of node calibrations and missing taxa", "topics": [ "make_mrbayes_runfile" ] }, { "page": "make_mrbayes_tree", "title": "Take a constraint tree and use mrBayes to get node ages and branch lengths given a set of node calibrations without any data.", "topics": [ "make_mrbayes_tree" ] }, { "page": "make_otol_associations", "title": "Associate Open Tree of Life authors with studies", "topics": [ "make_otol_associations" ] }, { "page": "make_overlap_table", "title": "Create an overlap table", "topics": [ "make_overlap_table" ] }, { "page": "make_sdm", "title": "Make a Super Distance Matrix (SDM) from a list of good matrices obtained with 'get_goodmatrices()'", "topics": [ "make_sdm" ] }, { "page": "make_treebase_associations", "title": "Associate TreeBase authors with studies", "topics": [ "make_treebase_associations" ] }, { "page": "make_treebase_cache", "title": "Create a cache from TreeBase", "topics": [ "make_treebase_cache" ] }, { "page": "map_nodes_ott", "title": "Add Open Tree of Life Taxonomy to tree nodes.", "topics": [ "map_nodes_ott" ] }, { "page": "match_all_calibrations", "title": "Match calibrations to nodes of a given tree", "topics": [ "match_all_calibrations" ] }, { "page": "matrices_to_table", "title": "Go from a list of patristic distance matrix to a table of node ages", "topics": [ "matrices_to_table" ] }, { "page": "matrix_to_table", "title": "Go from a patristic distance matrix to a node ages table", "topics": [ "matrix_to_table" ] }, { "page": "message_multiphylo", "title": "Message for a 'multiPhylo' input", "topics": [ "message_multiphylo" ] }, { "page": "missing_taxa_check", "title": "Checks that missing_taxa argument is ok to be used by make_mrbayes_runfile inside tree_add_dates functions.", "topics": [ "missing_taxa_check" ] }, { "page": "mrca_calibrations", "title": "Identify nodes of a tree topology that are most recent common ancestor (mrca) of taxon pairs from a 'calibrations' object", "topics": [ "mrca_calibrations" ] }, { "page": "opentree_chronograms", "title": "Chronogram database", "topics": [ "opentree_chronograms" ] }, { "page": "patristic_matrix_array_congruify", "title": "'patristic_matrix_array_congruify' is used for patristic_matrix_array_subset_both and patristic_matrix_array_congruify.", "topics": [ "patristic_matrix_array_congruify" ] }, { "page": "patristic_matrix_array_phylo_congruify", "title": "Congruify a patristic matrix array from a given 'phylo' object.", "topics": [ "patristic_matrix_array_phylo_congruify" ] }, { "page": "patristic_matrix_array_split", "title": "Split a patristic matrix array Used inside: patristic_matrix_array_congruify", "topics": [ "patristic_matrix_array_split" ] }, { "page": "patristic_matrix_array_subset", "title": "Subset a patristic matrix array", "topics": [ "patristic_matrix_array_subset" ] }, { "page": "patristic_matrix_array_subset_both", "title": "Are all desired taxa in the patristic matrix array?", "topics": [ "patristic_matrix_array_subset_both" ] }, { "page": "patristic_matrix_list_to_array", "title": "Convert list of patristic matrices to a 3D array.", "topics": [ "patristic_matrix_list_to_array" ] }, { "page": "patristic_matrix_MRCA", "title": "Get time of MRCA from patristic matrix. Used in 'datelife_result_MRCA()'.", "topics": [ "patristic_matrix_MRCA" ] }, { "page": "patristic_matrix_name_order_test", "title": "Test the name order of a patristic matrix so that row and column labels are in alphabetical order.", "topics": [ "patristic_matrix_name_order_test" ] }, { "page": "patristic_matrix_name_reorder", "title": "Reorder a matrix so that row and column labels are in alphabetical order.", "topics": [ "patristic_matrix_name_reorder" ] }, { "page": "patristic_matrix_pad", "title": "Fill in empty cells in a patristic matrix for missing taxa.", "topics": [ "patristic_matrix_pad" ] }, { "page": "patristic_matrix_taxa_all_matching", "title": "Are all desired taxa in the patristic matrix?", "topics": [ "patristic_matrix_taxa_all_matching" ] }, { "page": "patristic_matrix_to_newick", "title": "Convert patristic matrix to a newick string. Used inside: summarize_datelife_result.", "topics": [ "patristic_matrix_to_newick" ] }, { "page": "patristic_matrix_to_phylo", "title": "Convert a patristic matrix to a 'phylo' object.", "topics": [ "patristic_matrix_to_phylo" ] }, { "page": "patristic_matrix_unpad", "title": "Function to remove missing taxa from a 'datelifeResult' object.", "topics": [ "patristic_matrix_unpad" ] }, { "page": "phylo_check", "title": "Checks if 'phy' is a 'phylo' object and/or a chronogram.", "topics": [ "phylo_check" ] }, { "page": "phylo_congruify", "title": "Congruify a reference tree and a target tree given as 'phylo' objects.", "topics": [ "phylo_congruify" ] }, { "page": "phylo_generate_uncertainty", "title": "Generate uncertainty in branch lengths using a lognormal.", "topics": [ "phylo_generate_uncertainty" ] }, { "page": "phylo_get_node_numbers", "title": "Gets node numbers from any phylogeny", "topics": [ "phylo_get_node_numbers" ] }, { "page": "phylo_get_subset_array", "title": "Get a subset array from a 'phylo' object", "topics": [ "phylo_get_subset_array" ] }, { "page": "phylo_get_subset_array_congruify", "title": "Get a congruified subset array from a 'phylo' object", "topics": [ "phylo_get_subset_array_congruify" ] }, { "page": "phylo_has_brlen", "title": "Check if a tree has branch lengths", "topics": [ "phylo_has_brlen" ] }, { "page": "phylo_prune_missing_taxa", "title": "Prune missing taxa from a 'phylo' object Used inside phylo_get_subset_array and phylo_get_subset_array_congruify.", "topics": [ "phylo_prune_missing_taxa" ] }, { "page": "phylo_subset_both", "title": "Subset a reference and a target tree given as 'phylo' objects.", "topics": [ "phylo_subset_both" ] }, { "page": "phylo_tiplabel_space_to_underscore", "title": "Convert spaces to underscores in trees.", "topics": [ "phylo_tiplabel_space_to_underscore" ] }, { "page": "phylo_tiplabel_underscore_to_space", "title": "Convert underscores to spaces in trees.", "topics": [ "phylo_tiplabel_underscore_to_space" ] }, { "page": "phylo_to_patristic_matrix", "title": "Get a patristic matrix from a 'phylo' object.", "topics": [ "phylo_to_patristic_matrix" ] }, { "page": "pick_grove", "title": "Pick a grove in the case of multiple groves in a set of trees.", "topics": [ "pick_grove" ] }, { "page": "plant_bold_otol_tree", "title": "Some plants chronogram", "topics": [ "plant_bold_otol_tree" ] }, { "page": "problems", "title": "Problematic chronograms from Open Tree of Life.", "topics": [ "problems" ] }, { "page": "recover_mrcaott", "title": "Get an mrcaott tag from an OpenTree induced synthetic tree and get its name and ott id", "topics": [ "recover_mrcaott" ] }, { "page": "relevant_curators_tabulate", "title": "Return the relevant curators for a set of studies.", "topics": [ "relevant_curators_tabulate" ] }, { "page": "results_list_process", "title": "Take results_list and process it.", "topics": [ "results_list_process" ] }, { "page": "run", "title": "Core function to generate results", "topics": [ "run" ] }, { "page": "run_mrbayes", "title": "Runs MrBayes from R", "topics": [ "run_mrbayes" ] }, { "page": "sample_trees", "title": "Sample trees from a file containing multiple trees. Usually from a bayesian analysis output trees file.", "topics": [ "sample_trees" ] }, { "page": "some_ants_datelife_result", "title": "datelifeResult object of some ants", "topics": [ "some_ants_datelife_result" ] }, { "page": "subset2_search", "title": "A list with datelifeQuery and datelifeResult objects from a search of taxon names from subset2_taxa", "topics": [ "subset2_search" ] }, { "page": "subset2_taxa", "title": "Long list of >2.7k virus, bacteria, plant and animal taxon names", "topics": [ "subset2_taxa" ] }, { "page": "summarize_congruifiedCalibrations", "title": "Get summary statistics of ages in a 'congruifiedCalibrations' object.", "topics": [ "summarize_congruifiedCalibrations" ] }, { "page": "summarize_datelife_result", "title": "Summarize a 'datelifeResult' object.", "topics": [ "summarize_datelife_result" ] }, { "page": "summarize_fossil_range", "title": "Summarize taxon age from PBDB to just a single min and max age", "topics": [ "summarize_fossil_range" ] }, { "page": "summarize_summary_matrix", "title": "Gets all ages per taxon pair from a distance matrix Internal function used in summary_matrix_to_phylo_all().", "topics": [ "summarize_summary_matrix" ] }, { "page": "summary_matrix_to_phylo", "title": "Go from a summary matrix to an ultrametric 'phylo' object.", "topics": [ "summary_matrix_to_phylo" ] }, { "page": "summary_matrix_to_phylo_all", "title": "Get minimum, median, mean, midpoint, and maximum summary chronograms from a summary matrix of a 'datelifeResult' object.", "topics": [ "summary_matrix_to_phylo_all" ] }, { "page": "summary_patristic_matrix_array", "title": "Summarize patristic matrix array (by default, median). Used inside: summarize_datelife_result.", "topics": [ "summary_patristic_matrix_array" ] }, { "page": "summary.datelifeResult", "title": "Summarize a 'datelifeResult' object.", "topics": [ "summary.datelifeResult" ] }, { "page": "summary.matchedCalibrations", "title": "Summarize a 'matchedCalibrations' object 'summary.matchedCalibrations' gets the node age distribution from a 'matchedCalibrations' object.", "topics": [ "summary.matchedCalibrations" ] }, { "page": "threebirds_dr", "title": "'datelifeResult' object of three birds \"Rhea americana\", \"Pterocnemia pennata\", and \"Struthio camelus\"", "topics": [ "threebirds_dr" ] }, { "page": "tnrs_match", "title": "Taxon name resolution service (tnrs) applied to a vector of names by batches", "topics": [ "tnrs_match", "tnrs_match.default", "tnrs_match.phylo" ] }, { "page": "tree_add_dates", "title": "Add missing taxa to a dated tree and fabricate node ages for these missing taxa.", "topics": [ "tree_add_dates" ] }, { "page": "tree_add_nodelabels", "title": "Adds labels to nodes with no assigned label", "topics": [ "tree_add_nodelabels" ] }, { "page": "tree_add_outgroup", "title": "Function to add an outgroup to any phylogeny, in phylo or newick format", "topics": [ "tree_add_outgroup" ] }, { "page": "tree_check", "title": "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", "topics": [ "tree_check" ] }, { "page": "tree_fix_brlen", "title": "Take a tree with branch lengths and fix negative or zero length branches.", "topics": [ "tree_fix_brlen" ] }, { "page": "tree_from_taxonomy", "title": "Gets a taxonomic tree from a vector of taxa", "topics": [ "tree_from_taxonomy" ] }, { "page": "tree_get_node_data", "title": "Get node numbers, node names, descendant tip numbers and labels of nodes from any tree, and node ages from dated trees.", "topics": [ "tree_get_node_data" ] }, { "page": "tree_get_singleton_outgroup", "title": "Identify the presence of a single lineage outgroup in a phylogeny", "topics": [ "tree_get_singleton_outgroup" ] }, { "page": "tree_node_tips", "title": "To get tip numbers descending from any given node of a tree", "topics": [ "tree_node_tips" ] }, { "page": "treebase_cache", "title": "Information on contributors, authors, study ids and clades from studies with chronograms in Open tree of Life", "topics": [ "treebase_cache" ] }, { "page": "update_all_cached", "title": "Update all data files as data objects for the package", "topics": [ "update_all_cached" ] }, { "page": "update_datelife_cache", "title": "Create an updated OpenTree chronograms database object", "topics": [ "update_datelife_cache" ] }, { "page": "use_all_calibrations", "title": "Date a given tree topology using a given set of congruified calibrations or ages", "topics": [ "use_all_calibrations" ] }, { "page": "use_calibrations", "title": "Date a given tree topology using a combined set of given calibrations", "topics": [ "use_calibrations" ] }, { "page": "use_calibrations_bladj", "title": "Use calibrations to date a topology with the BLADJ algorithm.", "topics": [ "use_calibrations_bladj" ] }, { "page": "use_calibrations_bladj.matchedCalibrations", "title": "Use calibrations to date a topology with the BLADJ algorithm.", "topics": [ "use_calibrations_bladj.matchedCalibrations" ] }, { "page": "use_calibrations_each", "title": "Date a given tree topology by using a given list of calibrations independently, to generate multiple hypothesis of time of divergence", "topics": [ "use_calibrations_each" ] }, { "page": "use_calibrations_pathd8", "title": "Date a tree with secondary calibrations using PATHd8", "topics": [ "use_calibrations_pathd8" ] }, { "page": "use_calibrations_treePL", "title": "Date a tree with initial branch lengths with treePL.", "topics": [ "use_calibrations_treePL" ] } ], "_readme": "https://github.com/phylotastic/datelife/raw/HEAD/README.md", "_rundeps": [ "abind", "ade4", "ape", "askpass", "backports", "bibtex", "BiocManager", "bitops", "bold", "checkmate", "cli", "cluster", "clusterGeneration", "coda", "codetools", "colorspace", "combinat", "compare", "cpp11", "crayon", "crul", "curl", "data.table", "DEoptim", "deSolve", "digest", "doParallel", "dplyr", "expm", "foreach", "future", "future.apply", "geiger", "generics", "globals", "glue", "hms", "httpcode", "httr", "igraph", "ips", "iterators", "jsonlite", "knitcitations", "lattice", "lifecycle", "listenv", "lubridate", "magrittr", "maps", "MASS", "Matrix", "mime", "mnormt", "mvtnorm", "natserv", "ncbit", "nlme", "numDeriv", "openssl", "optimParallel", "osqp", "paleotree", "parallelly", "phangorn", "phylobase", "phylocomr", "phytools", "pillar", "pixmap", "pkgconfig", "plyr", "png", "prettyunits", "progress", "progressr", "purrr", "R6", "Rcpp", "RcppArmadillo", "RCurl", "RefManageR", "rentrez", "reshape2", "ritis", "rlang", "rncl", "RNeXML", "rotl", "rredlist", "S7", "scatterplot3d", "solrium", "sp", "stringi", "stringr", "subplex", "sys", "taxize", "tibble", "tidyr", "tidyselect", "timechange", "treebase", "triebeard", "urltools", "utf8", "uuid", "vctrs", "WikipediR", "wikitaxa", "withr", "worrms", "XML", "xml2", "zoo" ], "_vignettes": [ { "source": "fringiliidae.Rmd", "filename": "fringiliidae.html", "title": "Case study: the true finches", "engine": "knitr::rmarkdown", "headings": [ "1. Getting species names within the family Fringillidae", "2. Search the species names across a chronogram database", "3. Summarizing a datelifeResult object", "3.1 Source chronograms:", "To see how different datelife queries are made, check out the next tutorial vignette: Making a datelife query." ], "created": "2022-01-14 06:15:49", "modified": "2024-04-26 05:47:57", "commits": 5 }, { "source": "Getting_started_with_datelife.Rmd", "filename": "Getting_started_with_datelife.html", "title": "Getting started", "engine": "knitr::rmarkdown", "headings": [ "What can you get with datelife?", "How do you use datelife to get these data?", "1. Processing your organism names", "a) From a set of organism taxonomic names", "b) From a tree with organism taxonomic names as tip labels", "2. Searching the chronogram database", "3. Summarizing chronogram search results", "Citations", "MRCA ages", "Newick strings", "phylo objects", "Summary tables", "To see an application of these functions in a case study, check out the next tutorial vignette: Case Study: the true finches." ], "created": "2021-12-09 09:15:33", "modified": "2024-04-26 05:47:57", "commits": 10 }, { "source": "make_datelife_query.Rmd", "filename": "make_datelife_query.html", "title": "Making a DateLife query", "engine": "knitr::rmarkdown", "headings": [ "When input is list or vector of taxon names", "When input names are not found in the taxonomy", "Subspecies can also be searched", "Choosing between homonyms", "Making a query from an inclusive taxonomic group", "The function get_opentree_species()", "To see how trees with branch lengths estimated from BOLD (Barcode Of Life Database) data can be made with a datelife workflow, check out the next tutorial vignette: Estimating Branch Lengths." ], "created": "2022-12-13 00:13:54", "modified": "2024-04-26 05:47:57", "commits": 4 }, { "source": "making_bold_trees.Rmd", "filename": "making_bold_trees.html", "title": "Estimating initial branch lengths", "engine": "knitr::rmarkdown", "headings": [ "Using OpenTree topology:" ], "created": "2022-12-26 21:11:43", "modified": "2022-12-26 21:11:43", "commits": 1 } ], "_score": 6.169791953876032, "_indexed": true, "_nocasepkg": "datelife", "_universes": [ "phylotastic", "lunasare" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.6.9", "date": "2026-06-02T19:08:34.000Z", "distro": "noble", "commit": "e1ff3e41f4e41ad79b060cdfc974dd893eee9ff3", "fileid": "169e26cff13fce64fd4e21427902ca4ed62b048cad5af31f71f683f3bd92c1ca", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841490491" }, { "r": "4.6.0", "os": "linux", "version": "0.6.9", "date": "2026-06-02T19:08:33.000Z", "distro": "noble", "commit": "e1ff3e41f4e41ad79b060cdfc974dd893eee9ff3", "fileid": "d96b1c53f0c4c165f8139c1da36abcedc0801e7ac4d3aacf55045119359c2042", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841490491" }, { "r": "4.5.3", "os": "mac", "version": "0.6.9", "date": "2026-06-02T19:10:52.000Z", "commit": "e1ff3e41f4e41ad79b060cdfc974dd893eee9ff3", "fileid": "849926a43c8b66f036d9ecc5b04650f1a8a85462c8e937a9118ccc4c2fd9c4ec", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841490491" }, { "r": "4.6.0", "os": "mac", "version": "0.6.9", "date": "2026-06-02T19:10:38.000Z", "commit": "e1ff3e41f4e41ad79b060cdfc974dd893eee9ff3", "fileid": "e6b0e5a59295c0f3f6419ca943679c0c61a11ef5bff4359e9c7acc8e89f93cdc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841490491" }, { "r": "4.6.0", "os": "wasm", "version": "0.6.9", "date": "2026-06-02T19:08:40.000Z", "commit": "e1ff3e41f4e41ad79b060cdfc974dd893eee9ff3", "fileid": "09fd84a16aa5f777e656323b81949d03954b74f86d60ee7ed0f115825aa1595e", "status": "success", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841490491" }, { "r": "4.7.0", "os": "win", "version": "0.6.9", "date": "2026-06-02T19:07:07.000Z", "commit": "e1ff3e41f4e41ad79b060cdfc974dd893eee9ff3", "fileid": "1a2c932d16d6f561fc1f4e1410663e31aacc8f893c97b37fdc4886d5d410ff40", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841490491" }, { "r": "4.5.3", "os": "win", "version": "0.6.9", "date": "2026-06-02T19:07:07.000Z", "commit": "e1ff3e41f4e41ad79b060cdfc974dd893eee9ff3", "fileid": "4f85530792af702ba187d1fe5b5dfa892be8e00b5be1063c8673c8e177e36118", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841490491" }, { "r": "4.6.0", "os": "win", "version": "0.6.9", "date": "2026-06-02T19:08:07.000Z", "commit": "e1ff3e41f4e41ad79b060cdfc974dd893eee9ff3", "fileid": "c87e99615b1e1cbca105fa848e85cc308a2dcb5c2a67a63526b584a999e9b5dc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841490491" } ] }