Files in phylotastic/datelife
Scientific Data on Time of Lineage Divergence for Your Taxa

.Rbuildignore

.gitattributes

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.gitignore

.travis.yml

CRAN-SUBMISSION

DESCRIPTION

NAMESPACE

NEWS.md

R/.lintr

R/bold_data.R R/bold_tree.R R/cacheauthors.R R/calibrations_congruify.R R/calibrations_extract.R R/calibrations_get.R R/calibrations_match.R R/calibrations_mrca.R R/calibrations_use.R R/data.R R/datelife_calibrations.R R/datelife_internal.R R/datelife_median.R R/datelife_query.R R/datelife_query2.R R/datelife_query_tnrs.R R/datelife_result.R R/datelife_sdm.R R/datelife_search.R R/datelife_summary.R R/datelife_use.R R/get_species_from_ott.R R/groves.R R/lonely_functions.R R/make_bladj_tree.R R/make_mrbayes_tree.R R/matrix_to_table.R R/messages.R R/opentree_chronograms.R R/opentree_taxonomy.R R/opentree_taxonomy_general.R R/otol_tree.R R/pkg_reports_functions.R R/print.R R/result.R R/summary.R R/to_newick.R R/to_phylo.R R/to_phylo_all.R R/tree_add_dates.R R/tree_fix_brlen.R R/tree_from_taxonomy.R R/tree_processing.R R/uncertainty.R R/use_calibrations_bladj.R R/use_calibrations_bladj_matched.R R/use_calibrations_pathd8.R R/use_calibrations_treePL.R README.Rmd README.md

_pkgdown.yml

codecov.yml

cran-comments.md

data-raw/.DS_Store

data-raw/Agave5_14Nov13.TreeAnnOut_nombresPub

data-raw/Getting_started_with_datelife.md data-raw/README.md data-raw/Three_birds_LTTplot_phyloall.pdf data-raw/Tools_for_package_development.Rmd

data-raw/all_sources.txt

data-raw/axisGeo2.R data-raw/axisGeo3.R

data-raw/bm_map_nodes_ott-mbm.rda

data-raw/bm_map_nodes_ott-tot_time_list.rda

data-raw/bm_map_nodes_ott.R data-raw/cov.R data-raw/coverage.R data-raw/creating_datelife.R data-raw/datelife.Rmd data-raw/datelife_examples.Rmd data-raw/datelife_hexsticker.R data-raw/datelife_workflow.Rmd data-raw/fagales_mrp.pdf data-raw/fagales_mrp_fan.pdf data-raw/fagales_mrp_radial.pdf

data-raw/figures/baseplot.png

data-raw/figures/darwin-i-think.png

data-raw/figures/datelife-hex-empty.png

data-raw/figures/datelife-hex-rightward-black.png

data-raw/figures/datelife-hex-rightward-gray.png

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data-raw/figures/datelife-hex-upwards.png

data-raw/figures/datelife-hex.png

data-raw/hexsticker-datelife.ai

data-raw/hextsicker_env.R

data-raw/lttplot_phyloall_colors.txt

data-raw/my_tests.R

data-raw/names.txt

data-raw/non-ascii-check.R

data-raw/ott_id_problems.csv

data-raw/ott_id_problems_10.csv

data-raw/ott_id_problems_5.csv

data-raw/ott_id_problems_500.csv

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data-raw/test_taxa_batch.R data-raw/tests.R data-raw/vignette_making_bladj_trees.Rmd data-raw/workflow_diagrams/congruify_workflow_datelife_search.pdf data-raw/workflow_diagrams/congruify_workflow_tree_add_dates.pdf data-raw/workflow_diagrams/congruify_workflow_use_all_calibrations.pdf data-raw/workflow_diagrams/datelife_workflow_diagrams_2018.07.12.R data-raw/workflow_diagrams/datelife_workflows copy.pdf data-raw/workflow_diagrams/datelife_workflows.pdf

data-raw/workflow_diagrams/datelife_workflows.pptx

data-raw/workflow_diagrams/use_all_calibrations_foodweb1.pdf

data/birds_and_cats.rda

data/contributor_cache.rda

data/cov.rda

data/felid_gdr_phylo_all.rda

data/felid_sdm.rda

data/opentree_chronograms.rda

data/plant_bold_otol_tree.rda

data/problems.rda

data/some_ants_datelife_result.rda

data/subset2_search.rda

data/subset2_taxa.rda

data/threebirds_dr.rda

data/treebase_cache.rda

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inst/CITATION

inst/CITATION.cff

inst/WORDLIST

inst/pkgdown.yml

man/birds_and_cats.Rd man/build_grove_list.Rd man/build_grove_matrix.Rd man/check_conflicting_calibrations.Rd man/check_ott_input.Rd man/choose_cluster.Rd man/classification_paths_from_taxonomy.Rd man/clean_ott_chronogram.Rd man/clean_taxon_info_children.Rd man/clean_tnrs.Rd man/cluster_patristicmatrix.Rd man/congruify_and_check.Rd man/congruify_and_mrca_multiPhylo.Rd man/congruify_and_mrca_phylo.Rd man/contributor_cache.Rd man/date_with_pbdb.Rd man/datelife_authors_tabulate.Rd man/datelife_result_MRCA.Rd man/datelife_result_median.Rd man/datelife_result_median_matrix.Rd man/datelife_result_sdm_matrix.Rd man/datelife_result_sdm_phylo.Rd man/datelife_result_study_index.Rd man/datelife_result_variance_matrix.Rd man/datelife_search.Rd man/datelife_use.Rd man/datelife_use_datelifequery.Rd man/dot-get_ott_lineage.Rd man/extract_calibrations_dateliferesult.Rd man/extract_calibrations_phylo.Rd man/extract_ott_ids.Rd man/felid_gdr_phylo_all.Rd man/felid_sdm.Rd

man/figures/datelife-hex-upwards-gray.png

man/figures/datelife-hexsticker-ai.png

man/figures/datelife-hexsticker-latest.png

vignettes/.gitignore

vignettes/Getting_started_with_datelife.Rmd vignettes/README.R vignettes/fringiliidae.Rmd vignettes/make_datelife_query.Rmd vignettes/making_bold_trees.Rmd

vignettes/making_bold_trees.Rmd.orig

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phylotastic/datelife documentation built on June 9, 2024, 6:50 p.m.

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phylotastic/datelife
Scientific Data on Time of Lineage Divergence for Your Taxa

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Scientific Data on Time of Lineage Divergence for Your Taxa

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