bomeara. See also theR-universe documentation.Package: closesamples 1.0
Brian C. OMeara
closesamples: Gets feasible taxon samples on a tree
Often you want to pick species at random, but don't have access to all the possible species, and your group might be a nonrandom set. However, you might have a taxonomy, perhaps a bad one, for all the species. This will let you pick species at random on that full taxonomy and then pick a species out of the possible set closest to this. You could still have a biased sample, but way less biased.
Authors:
closesamples_1.0.tar.gz
closesamples_1.0.tgz(r-4.4-any)closesamples_1.0.tgz(r-4.3-any)
closesamples_1.0.tar.gz(r-4.5-noble)closesamples_1.0.tar.gz(r-4.4-noble)
closesamples_1.0.tgz(r-4.4-emscripten)closesamples_1.0.tgz(r-4.3-emscripten)
closesamples.pdf |closesamples.html✨
closesamples/json (API)
| # Install 'closesamples' in R: |
| install.packages('closesamples', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bomeara/closesamples/issues
Last updated 3 years agofrom:1beb4a721e. 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:GetClosestSamplesGetEnclosingTaxonomyLabelNodesWithFeasibleDescendantsSubsampleTree
Dependencies:apeaskpassassertthatbackportsbase64encbitbit64boldbslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncrulcurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomeforeachforeignFormulafsgenericsggplot2gluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobanditeratorsjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnatservnlmennetopensslpbapplyphangornpillarpkgconfigplyrprettyunitsprogresspurrrquadprogR6rappdirsratelimitrRColorBrewerRcppRcppArmadilloRcppGSLRcppParallelRcppZigguratreadrrentrezrexRfastRfast2ritisrlangrmarkdownRnanoflannrnclrotlrpartrredlistrstudioapisassscalessolriumstringistringrsystaxizetibbletidyselecttinytextriebeardtzdburltoolsutf8vctrsviridisviridisLitevroomWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2yamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get the closest taxon to the focal taxon | GetClosest |
| Get n samples | GetClosestSamples |
| Get enclosing taxonomy for a feasible tree | GetEnclosingTaxonomy |
| Get similarity Uses ape's cophenetic.phylo to get patristic distances between pairs of taxa, then makes the diagonals Inf. If the tree has no branch lengths, makes every edge length 1. | GetSimilarity |
| Include descendant taxon ids in node labels | LabelNodesWithChosenDescendants |
| Include descendant taxon ids in node labels | LabelNodesWithFeasibleDescendants |
| Return a sampled tree | SubsampleTree |
