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datelife
View on CRAN: Click
here
Download and install datelife package within the R console
Install from CRAN:
install.packages("datelife")
Install from Github:
library("remotes")
install_github("cran/datelife")
Install by package version:
library("remotes")
install_version("datelife", "0.6.8")
Attach the package and use:
library("datelife")
Maintained by
Luna L. Sanchez Reyes
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
First Published: 2022-01-17
Latest Update: 2023-06-19
Description:
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 . 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) .
To find the grove of chronograms with a sufficiently overlapping set of taxa
for summarizing, we implement theorem 1.1. from An
How to cite:
Luna L. Sanchez Reyes (2022). datelife: Scientific Data on Time of Lineage Divergence for Your Taxa. R package version 0.6.8, https://cran.r-project.org/web/packages/datelife. Accessed 24 Apr. 2025.
Previous versions and publish date:
Other packages that cited datelife R package
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Other R packages that datelife depends,
imports, suggests or enhances
Functions, R codes and Examples using
the datelife R package
Some associated functions: birds_and_cats . build_grove_list . build_grove_matrix . check_conflicting_calibrations . check_ott_input . choose_cluster . classification_paths_from_taxonomy . clean_ott_chronogram . clean_taxon_info_children . clean_tnrs . cluster_patristicmatrix . congruify_and_check . congruify_and_mrca_multiPhylo . congruify_and_mrca_phylo . contributor_cache . date_with_pbdb . datelife_authors_tabulate . datelife_result_MRCA . datelife_result_median . datelife_result_median_matrix . datelife_result_sdm_matrix . datelife_result_sdm_phylo . datelife_result_study_index . datelife_result_variance_matrix . datelife_search . datelife_use . datelife_use_datelifequery . dot-get_ott_lineage . extract_calibrations_dateliferesult . extract_calibrations_phylo . extract_ott_ids . felid_gdr_phylo_all . felid_sdm . 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_synthetic_tree . get_ott_children . get_ott_clade . get_ott_lineage . get_subset_array_dispatch . 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_all_associations . make_bladj_tree . make_bold_otol_tree . make_contributor_cache . make_datelife_query . make_datelife_query2 . make_mrbayes_runfile . make_mrbayes_tree . make_otol_associations . make_overlap_table . make_sdm . make_treebase_associations . make_treebase_cache . map_nodes_ott . match_all_calibrations . matrices_to_table . matrix_to_table . message_multiphylo . missing_taxa_check . mrca_calibrations . opentree_chronograms . patristic_matrix_MRCA . patristic_matrix_array_congruify . patristic_matrix_array_phylo_congruify . patristic_matrix_array_split . patristic_matrix_array_subset . patristic_matrix_array_subset_both . patristic_matrix_list_to_array . patristic_matrix_name_order_test . patristic_matrix_name_reorder . patristic_matrix_pad . patristic_matrix_taxa_all_matching . patristic_matrix_to_newick . patristic_matrix_to_phylo . patristic_matrix_unpad . phylo_check . phylo_congruify . phylo_generate_uncertainty . phylo_get_node_numbers . phylo_get_subset_array . phylo_get_subset_array_congruify . phylo_has_brlen . phylo_prune_missing_taxa . phylo_subset_both . phylo_tiplabel_space_to_underscore . phylo_tiplabel_underscore_to_space . phylo_to_patristic_matrix . pick_grove . plant_bold_otol_tree . problems . recover_mrcaott . relevant_curators_tabulate . results_list_process . run . run_mrbayes . sample_trees . some_ants_datelife_result . subset2_search . subset2_taxa . summarize_congruifiedCalibrations . summarize_datelife_result . summarize_fossil_range . summarize_summary_matrix . summary.datelifeResult . summary.matchedCalibrations . summary_matrix_to_phylo . summary_matrix_to_phylo_all . summary_patristic_matrix_array . threebirds_dr . tnrs_match . tree_add_dates . tree_add_nodelabels . tree_add_outgroup . tree_check . tree_fix_brlen . tree_from_taxonomy . tree_get_node_data . tree_get_singleton_outgroup . tree_node_tips . treebase_cache . update_all_cached . update_datelife_cache . use_all_calibrations . use_calibrations . use_calibrations_bladj.matchedCalibrations . use_calibrations_bladj . use_calibrations_each . use_calibrations_pathd8 . use_calibrations_treePL .
Some associated R codes: bold_data.R . bold_tree.R . cacheauthors.R . calibrations_congruify.R . calibrations_extract.R . calibrations_get.R . calibrations_match.R . calibrations_mrca.R . calibrations_use.R . data.R . datelife_calibrations.R . datelife_internal.R . datelife_median.R . datelife_query.R . datelife_query2.R . datelife_query_tnrs.R . datelife_result.R . datelife_sdm.R . datelife_search.R . datelife_summary.R . datelife_use.R . get_species_from_ott.R . groves.R . lonely_functions.R . make_bladj_tree.R . make_mrbayes_tree.R . matrix_to_table.R . messages.R . opentree_chronograms.R . opentree_taxonomy.R . opentree_taxonomy_general.R . otol_tree.R . pkg_reports_functions.R . print.R . result.R . summary.R . to_newick.R . to_phylo.R . to_phylo_all.R . tree_add_dates.R . tree_fix_brlen.R . tree_from_taxonomy.R . tree_processing.R . uncertainty.R . use_calibrations_bladj.R . use_calibrations_bladj_matched.R . use_calibrations_pathd8.R . use_calibrations_treePL.R . Full datelife package functions and examples
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