Package: phyloTop 2.1.2
Michelle Kendall
phyloTop: Calculating Topological Properties of Phylogenies
Tools for calculating and viewing topological properties of phylogenetic trees.
Authors:
phyloTop_2.1.2.tar.gz
phyloTop_2.1.2.zip(r-4.5)phyloTop_2.1.2.zip(r-4.4)phyloTop_2.1.2.zip(r-4.3)
phyloTop_2.1.2.tgz(r-4.4-any)phyloTop_2.1.2.tgz(r-4.3-any)
phyloTop_2.1.2.tar.gz(r-4.5-noble)phyloTop_2.1.2.tar.gz(r-4.4-noble)
phyloTop_2.1.2.tgz(r-4.4-emscripten)phyloTop_2.1.2.tgz(r-4.3-emscripten)
phyloTop.pdf |phyloTop.html✨
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 site:https://michellekendall.github.io
Last updated 2 years agofrom:99ec9a919d. Checks:OK: 5 NOTE: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 07 2024 |
| R-4.5-win | NOTE | Dec 07 2024 |
| R-4.5-linux | NOTE | Dec 07 2024 |
| R-4.4-win | OK | Dec 07 2024 |
| R-4.4-mac | OK | Dec 07 2024 |
| R-4.3-win | OK | Dec 07 2024 |
| R-4.3-mac | OK | Dec 07 2024 |
Exports:avgLaddercherriescolless.phyloconfigShowgetDepthsgetLabGenealogyILnumberladderShowladderSizesmakeEpiRecordmakePhyloTreemaxHeightnConfignodeDepthnodeDepthFracnodeImbnodeImbFracphyloCheckphyloToppitchforksrtree4sackin.phylosplitTopstairssubtreeShowtreeImbwidths
Dependencies:abindade4apeaskpassbackportsbootbroomcarcarDataclicolorspacecowplotcpp11crayoncurlDerivdigestdoBydplyrfansifarverFormulagenericsggplot2gluegtablehmshttrigraphisobandjsonlitelabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkmimeminqamodelrmunsellNHPoissonnlmenloptrnnetnumDerivopensslpbkrtestphylobasepillarpixmappkgconfigplyrprettyunitsprogresspurrrquantregR6RColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangrnclRNeXMLscalesspSparseMstringistringrsurvivalsystibbletidyrtidyselectutf8uuidvctrsviridisLitewithrXMLxml2
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 |
