Package: phyloTop 2.1.3
Michelle Kendall
phyloTop: Calculating Topological Properties of Phylogenies
Tools for calculating and viewing topological properties of phylogenetic trees.
Authors:
phyloTop_2.1.3.tar.gz
phyloTop_2.1.3.zip(r-4.7)phyloTop_2.1.3.zip(r-4.6)phyloTop_2.1.3.zip(r-4.5)
phyloTop_2.1.3.tgz(r-4.6-any)phyloTop_2.1.3.tgz(r-4.5-any)
phyloTop_2.1.3.tar.gz(r-4.7-any)phyloTop_2.1.3.tar.gz(r-4.6-any)
phyloTop_2.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
phyloTop/json (API)
NEWS
| # Install 'phyloTop' in R: |
| install.packages('phyloTop', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/michellekendall/phylotop/issues
Pkgdown/docs site:https://michellekendall.github.io
Last updated from:7043fa2d12. Checks:9 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 170 | ||
| source / vignettes | OK | 177 | ||
| linux-release-x86_64 | OK | 156 | ||
| macos-release-arm64 | OK | 85 | ||
| macos-oldrel-arm64 | OK | 82 | ||
| windows-devel | OK | 98 | ||
| windows-release | OK | 99 | ||
| windows-oldrel | OK | 108 | ||
| wasm-release | OK | 132 |
Exports:avgLaddercherriescolless.phyloconfigShowgetDepthsgetLabGenealogyILnumberladderShowladderSizesmakeEpiRecordmakePhyloTreemaxHeightnConfignodeDepthnodeDepthFracnodeImbnodeImbFracphyloCheckphyloToppitchforksrtree4sackin.phylosplitTopstairssubtreeShowtreeImbwidths
Dependencies:abindade4apeaskpassbackportsbootbroomcarcarDataclicolorspacecowplotcpp11crayoncurlDerivdigestdoBydplyrfarverforecastFormulafracdiffgenericsggplot2gluegtablehmshttrigraphisobandjsonlitelabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkmimeminqamodelrNHPoissonnlmenloptrnnetnumDerivopensslpbkrtestphylobasepillarpixmappkgconfigplyrprettyunitsprogresspurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2rlangrnclRNeXMLS7scalesspSparseMstringistringrsurvivalsystibbletidyrtidyselecttimeDateurcautf8uuidvctrsviridisLitewithrXMLxml2zoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Average ladder size | avgLadder |
| Cherry number | cherries |
| Colless number | colless.phylo |
| Plot a tree highlighting configurations | configShow |
| Find the depth of each node | getDepths |
| Create genealogy | getLabGenealogy |
| IL number | ILnumber |
| Show ladders | ladderShow |
| Ladder sizes | ladderSizes |
| Simulate epidemiological record | makeEpiRecord |
| Maximum tree height | maxHeight |
| Configuration sizes in a tree | nConfig |
| Node depth | nodeDepth |
| Fraction of nodes beyond a given depth | nodeDepthFrac |
| Node imbalance | nodeImb |
| Fraction of nodes with given imbalance | nodeImbFrac |
| phyloTop: topological properties of phylogenies | phyloTop |
| Number of pitchforks | pitchforks |
| Random phylo4 tree | rtree4 |
| Sackin index | sackin.phylo |
| Split topology | splitTop |
| Stairs | stairs |
| Highlight a subtree | subtreeShow |
| Tree imbalance | treeImb |
| Number of nodes at each depth | widths |
