Package: OpenTreeChronograms 2022.1.28

OpenTreeChronograms: Open Tree of Life Chronograms

Chronogram database constructed from Open Tree of Life's phylogenetic store.

Authors:Brian O'Meara [aut], Luna L. Sanchez Reyes [aut, cre]

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OpenTreeChronograms.pdf |OpenTreeChronograms.html✨
OpenTreeChronograms/json (API)
NEWS

# Install 'OpenTreeChronograms' in R:
install.packages('OpenTreeChronograms', repos = c('https://lunasare.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

27 exports 0.00 score 160 dependencies 5 scripts 228 downloads

Last updated 2 years agofrom:da8add3506. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 14 2024
R-4.5-winNOTESep 14 2024
R-4.5-linuxNOTESep 14 2024
R-4.4-winNOTESep 14 2024
R-4.4-macNOTESep 14 2024
R-4.3-winNOTESep 14 2024
R-4.3-macNOTESep 14 2024

Exports:check_ott_inputclassification_paths_from_taxonomyclean_ott_chronogramclean_taxon_info_childrenclean_tnrsdate_with_pbdbextract_ott_idsget_fossil_rangeget_opentree_chronogramsget_otol_chronogramsget_ott_childrenget_ott_cladeget_ott_lineageget_valid_childrenis_good_chronogramis_phylomake_all_associationsmake_contributor_cachemake_overlap_tablemap_nodes_ottphylo_has_brlenrecover_mrcaottsummarize_fossil_rangetnrs_matchtree_from_taxonomyupdate_all_cachedupdate_datelife_cache

Dependencies:apeaskpassassertthatbackportsbase64encbibtexbitbit64bitopsbslibcachemcheckmateclicliprclusterclusterGenerationcodacodetoolscolorspacecombinatconditionzcpp11crayoncredentialscrulcurldata.tableDEoptimdescdeSolvedigestdoParalleldplyrevaluateexpmfansifarverfastmapfastmatchfontawesomeforeachforeignFormulafsgeigergenericsgertggplot2ghgitcredsgluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttrhttr2igraphiniisobanditeratorsjquerylibjsonliteknitcitationsknitrlabelinglatticelazyevallifecyclelubridatemagrittrmapsMASSMatrixmemoisemgcvmimemnormtmunsellmvtnormnatservncbitnlmennetnumDerivopenssloptimParallelpaleotreepbapplyphangornphytoolspillarpkgconfigplyrpngprettyunitsprogresspurrrquadprogR6rappdirsratelimitrRColorBrewerRcppRCurlreadrRefManageRrentrezrexritisrlangrmarkdownrnclrotlrpartrprojrootrredlistrstudioapisassscalesscatterplot3dsolriumstringistringrsubplexsystaxizetibbletidyselecttimechangetinytextreebasetriebeardtzdburltoolsusethisutf8uuidvctrsviridisviridisLitevroomwhiskerWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2yamlzipzoo

Readme and manuals

Help Manual

Help pageTopics
Get the lineage of a set of taxa. '.get_ott_lineage' uses 'rotl::taxonomy_taxon_info()' with 'include_lineage = TRUE'..get_ott_lineage
Check input for other functionscheck_ott_input
Gets classification paths for a vector of taxaclassification_paths_from_taxonomy
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 unrootedclean_ott_chronogram
Identify, extract and clean taxonomic children names from a 'taxonomy_taxon_info()' output.clean_taxon_info_children
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.clean_tnrs
Date with Paleobiology Database and paleotree.date_with_pbdb
Get OTT ids from a character vector containing species names and OTT ids.extract_ott_ids extract_ott_ids.default
Get the ages for a taxon from PBDBget_fossil_range
Get all chronograms from Open Tree of Life databaseget_opentree_chronograms get_otol_chronograms
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 subtreeget_ott_children
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.get_ott_clade
Get the Open Tree of Life Taxonomic identifier (OTT id) and name of all lineages from one or more input taxa.get_ott_lineage
Extract valid children from given taxonomic name(s) or Open Tree of Life Taxonomic identifiers (OTT ids) from a taxonomic source.get_valid_children
Check if a tree is a valid chronogram.is_good_chronogram
Checks if 'phy' is a 'phylo' object and/or a chronogram.is_phylo
Find all authors and where they have deposited their treesmake_all_associations
Create a cache from Open Tree of Lifemake_contributor_cache
Associate Open Tree of Life authors with studiesmake_otol_associations
Create an overlap tablemake_overlap_table
Associate TreeBase authors with studiesmake_treebase_associations
Create a cache from TreeBasemake_treebase_cache
Add Open Tree of Life Taxonomy to tree nodes.map_nodes_ott
Open Tree of Life Chronogram database in Ropentree_chronograms
Check if a tree has branch lengthsphylo_has_brlen
Convert spaces to underscores in trees.phylo_tiplabel_space_to_underscore
Convert underscores to spaces in trees.phylo_tiplabel_underscore_to_space
Problematic chronograms from Open Tree of Life.problematic_chronograms
Get an mrcaott tag from an OpenTree induced synthetic tree and get its name and ott idrecover_mrcaott
Summarize taxon age from PBDB to just a single min and max agesummarize_fossil_range
Taxon name resolution service (tnrs) applied to a vector of names by batchestnrs_match tnrs_match.default tnrs_match.phylo
Gets a taxonomic tree from a vector of taxatree_from_taxonomy
Update all data files as data objects for the packageupdate_all_cached
Create an updated OpenTree chronograms database objectupdate_datelife_cache