Package: popularitree 0.0.0.9000
popularitree: Subsamples a tree to get popular taxa
Often you want to show a reduced summary tree. Taxa chosen should span all the tree (for example, a tree of mammals should not have just primates) but also be recognizable groups to your audience. This lets you select a final tree size you want, criteria you want to use, and finds the tree that maximizes the criteria.
Authors:
popularitree_0.0.0.9000.tar.gz
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popularitree.pdf |popularitree.html✨
popularitree/json (API)
# Install 'popularitree' in R: |
install.packages('popularitree', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bomeara/popularitree/issues
Last updated 7 years agofrom:ce3e5899c0. Checks:OK: 7. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 18 2024 |
R-4.5-win | OK | Aug 18 2024 |
R-4.5-linux | OK | Aug 18 2024 |
R-4.4-win | OK | Aug 18 2024 |
R-4.4-mac | OK | Aug 18 2024 |
R-4.3-win | OK | Aug 18 2024 |
R-4.3-mac | OK | Aug 18 2024 |
Exports:generate_samplepopularitreespecies_get_commonspecies_gtrends_popularityspecies_ncbi_common_existstree_compute_measurestree_convert_to_common
Dependencies:anytimeapeaskpassassertthatbackportsbase64encBHbitbit64boldbslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncrulcurldata.tabledigestdplyrevaluatefansifarverfastmapfastmatchfontawesomeforeachforeignFormulafsgenericsggplot2ggseqlogogluegridExtragtablegtrendsRhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobanditeratorsjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnatservnlmennetopensslpbapplypermutephangornpicantepillarpkgconfigplyrprettyunitsprogresspurrrquadprogR6rappdirsratelimitrRColorBrewerRcppreadrrentrezrexritisrlangrmarkdownrnclrotlrpartrredlistrstudioapisassscalessolriumstringistringrsystaxizetibbletidyselecttinytextriebeardtzdburltoolsutf8vctrsveganviridisviridisLitevroomWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2yamlzoo
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Generate a sample of species, weighted by their score | generate_sample |
Get a smaller tree with popular taxa spanning the diversity | popularitree |
Return common name if known, otherwise return scientific name | species_get_common |
Get a sum of hits of a species relative to a standard | species_gtrends_popularity |
Return 1 if a species has a common name in NCBI, 0 otherwise | species_ncbi_common_exists |
Compute popularity measures | tree_compute_measures |
Convert tips to common names if possible | tree_convert_to_common |