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.zip(r-4.7-any)popularitree_0.0.0.9000.zip(r-4.6-any)popularitree_0.0.0.9000.zip(r-4.5-any)
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popularitree_0.0.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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 from:ce3e5899c0. Checks:7 ERROR, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | ERROR | 166 | ||
| source / vignettes | OK | 474 | ||
| linux-release | ERROR | 202 | ||
| macos-release | ERROR | 131 | ||
| macos-oldrel | ERROR | 133 | ||
| windows-devel | ERROR | 98 | ||
| windows-release | ERROR | 141 | ||
| windows-oldrel | ERROR | 95 | ||
| wasm-release | OK | 134 |
Exports:generate_samplepopularitreespecies_get_commonspecies_gtrends_popularityspecies_ncbi_common_existstree_compute_measurestree_convert_to_common
Dependencies:anytimeapeaskpassbackportsBHcheckmatecliclustercodetoolscpp11crayoncrulcurldata.tabledigestdplyrfarverfuturefuture.applygenericsggplot2globalsgluegtablegtrendsRhmshttpcodehttrigraphisobandjsonlitelabelinglatticelifecyclelistenvmagrittrMASSMatrixmgcvmimenatservnlmeopensslosqpparallellypermutephangornpicantepillarpkgconfigplyrprettyunitsprogressprogressrR6RColorBrewerRcppRcppArmadillorentrezritisrlangrnclrotlrredlistS7scalessolriumstringisystaxizetibbletidyselecttriebeardurltoolsutf8vctrsveganviridisLiteWikipediRwikitaxawithrworrmsXMLxml2zoo
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 |