bomeara. See also theR-universe documentation.Package: popularitree 0.0.0.9000
Brian OMeara
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
popularitree_0.0.0.9000.tgz(r-4.4-any)popularitree_0.0.0.9000.tgz(r-4.3-any)
popularitree_0.0.0.9000.tar.gz(r-4.5-noble)popularitree_0.0.0.9000.tar.gz(r-4.4-noble)
popularitree_0.0.0.9000.tgz(r-4.4-emscripten)
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: 1 ERROR: 3. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 16 2024 |
| R-4.5-linux | ERROR | Dec 18 2024 |
| R-4.4-mac | ERROR | Nov 18 2024 |
| R-4.3-mac | ERROR | Nov 18 2024 |
Exports:generate_samplepopularitreespecies_get_commonspecies_gtrends_popularityspecies_ncbi_common_existstree_compute_measurestree_convert_to_common
Dependencies:anytimeapeaskpassassertthatbackportsbase64encBHbitbit64boldbslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncrulcurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomeforeachforeignFormulafsgenericsggplot2gluegridExtragtablegtrendsRhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobanditeratorsjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnatservnlmennetopensslpbapplypermutephangornpicantepillarpkgconfigplyrprettyunitsprogresspurrrquadprogR6rappdirsratelimitrRColorBrewerRcppRcppArmadilloreadrrentrezrexritisrlangrmarkdownrnclrotlrpartrredlistrstudioapisassscalessolriumstringistringrsystaxizetibbletidyselecttinytextriebeardtzdburltoolsutf8vctrsveganviridisviridisLitevroomWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2yamlzoo
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 |
