Trees are split by phylum | Starting from a higher taxon | A dated fish tree | Trees for a geographic area | Which backend should I use? | References
Package: aptg 0.4.0
Christophe Benjamin
aptg: Automatic Phylogenetic Tree Generator
Generates phylogenetic trees and distance matrices from a list of taxon names, or from a higher taxon expanded down to a chosen lower rank. Trees are obtained as induced subtrees of the Open Tree of Life synthetic tree using the 'rotl' package (Michonneau, Brown and Winter, 2016, <doi:10.1111/2041-210X.12593>). Expansion of a higher taxon to its descendants uses 'taxize' (Chamberlain and Szocs, 2013, <doi:10.12688/f1000research.2-191.v2>).
Authors:
aptg_0.4.0.tar.gz
aptg_0.4.0.tar.gz(r-4.7-any)aptg_0.4.0.tar.gz(r-4.6-any)
aptg_0.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
aptg/json (API)
| # Install 'aptg' in R: |
| install.packages('aptg', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/christophebenjamin/aptg/issues
Last updated from:87f167b8a2. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 135 | ||
| source / vignettes | OK | 253 | ||
| linux-release-x86_64 | OK | 153 | ||
| wasm-release | OK | 132 |
Exports:downto.treeregion.treetaxa.tree
Dependencies:apeaskpassclicpp11crayoncrulcurldata.tabledigestdplyrfastmatchgenericsgluehmshttpcodehttrigraphjsonlitelatticelifecyclemagrittrMatrixmimenatservnlmeopensslphangornpillarpkgconfigplyrprettyunitsprogressquadprogR6Rcpprentrezritisrlangrnclrotlrredlistsolriumstringisystaxizetibbletidyselecttriebeardurltoolsutf8vctrsWikipediRwikitaxawithrworrmsXMLxml2zoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Phylogenetic tree from a taxon down to a lower rank | downto.tree |
| Phylogenetic tree(s) for a taxon within a geographic area | region.tree |
| Phylogenetic trees and distance matrices from a list of taxa | taxa.tree |
