Package: phyloTop 2.1.2
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
Last updated 2 years agofrom:99ec9a919d. Checks:OK: 7. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 09 2024 |
R-4.5-win | OK | Aug 09 2024 |
R-4.5-linux | OK | Aug 09 2024 |
R-4.4-win | OK | Aug 09 2024 |
R-4.4-mac | OK | Aug 09 2024 |
R-4.3-win | OK | Aug 09 2024 |
R-4.3-mac | OK | Aug 09 2024 |
Exports:avgLaddercherriescolless.phyloconfigShowgetDepthsgetLabGenealogyILnumberladderShowladderSizesmakeEpiRecordmakePhyloTreemaxHeightnConfignodeDepthnodeDepthFracnodeImbnodeImbFracphyloCheckphyloToppitchforksrtree4sackin.phylosplitTopstairssubtreeShowtreeImbwidths
Dependencies:abindade4apeaskpassbackportsbootbroomcarcarDataclicolorspacecowplotcpp11crayoncurlDerivdigestdoBydplyrfansifarvergenericsggplot2gluegtablehmshttrigraphisobandjsonlitelabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkmimeminqamodelrmunsellNHPoissonnlmenloptrnnetnumDerivopensslpbkrtestphylobasepillarpixmappkgconfigplyrprettyunitsprogresspurrrquantregR6RColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangrnclRNeXMLscalesspSparseMstringistringrsurvivalsystibbletidyrtidyselectutf8uuidvctrsviridisLitewithrXMLxml2
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 |