Package: phylobase 0.8.12

Francois Michonneau

phylobase: Base Package for Phylogenetic Structures and Comparative Data

Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.

Authors:R Hackathon et al.

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phylobase.pdf |phylobase.html✨
phylobase/json (API)
NEWS

# Install 'phylobase' in R:

install.packages('phylobase', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fmichonneau/phylobase/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

geospiza - Data from Darwin's finches
geospiza_raw - Data from Darwin's finches
owls4 - 'Owls' data from ape

On CRAN:

phylogenetics

11.20 score 17 stars 18 packages 398 scripts 3.6k downloads 29 mentions 78 exports 49 dependencies

Last updated 10 months agofrom:5eecded489. Checks:OK: 9. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 25 2024
R-4.5-win-x86_64	OK	Oct 25 2024
R-4.5-linux-x86_64	OK	Oct 25 2024
R-4.4-win-x86_64	OK	Oct 25 2024
R-4.4-mac-x86_64	OK	Oct 25 2024
R-4.4-mac-aarch64	OK	Oct 25 2024
R-4.3-win-x86_64	OK	Oct 25 2024
R-4.3-mac-x86_64	OK	Oct 25 2024
R-4.3-mac-aarch64	OK	Oct 25 2024

Exports:[addData ancestor ancestors checkPhylo4 children depthTips descendants edgeId edgeLabels edgeLabels<-edgeLength edgeLength<-edgeOrder edges extractTree getEdge getNode hasDuplicatedLabels hasEdgeLabels hasEdgeLength hasNodeData hasNodeLabels hasPoly hasRetic hasSingle hasTipData head internalEdges isRooted isUltrametric labels labels<-MRCA names nData nEdges nNodes nodeData nodeData<-nodeDepth nodeHeight nodeId nodeLabels nodeLabels<-nodeType nTips phylo4 phylo4d phylobase.options phylobubbles phyloXXYY plot plotOneTree print prune readNCL readNewick readNexus reorder rootNode rootNode<-shortestPath show siblings subset sumEdgeLength summary tail tdata tdata<-terminalEdges tip.data.plot tipData tipData<-tipLabels tipLabels<-treePlot

Dependencies:ade4 ape askpass cli cpp11 crayon curl digest dplyr fansi generics glue hms httr jsonlite lattice lifecycle magrittr MASS mime nlme openssl pillar pixmap pkgconfig plyr prettyunits progress purrr R6 Rcpp RcppArmadillo reshape2 rlang rncl RNeXML sp stringi stringr sys tibble tidyr tidyselect utf8 uuid vctrs withr XML xml2

The phylo4 classes and methods

Ben Bolker, Peter Cowan, François Michonneau

Rendered fromphylobase.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2024-01-29
Started: 2024-01-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Utilities and Tools for Phylogenetics	phylobase-package phylobase
Adding data to a phylo4 or a phylo4d object	addData addData,phylo4-method addData,phylo4d-method addData-methods
Tree traversal and utility functions	ancestor ancestors children descendants siblings
Validity checking for phylo4 objects	checkPhylo4 checkPhylo4Data checkTree
Edges accessors	edgeOrder edgeOrder,phylo4-method edges edges,phylo4-method internalEdges internalEdges,phylo4-method terminalEdges terminalEdges,phylo4-method
Get tree from tree+data object	extractTree
Format data for use in phylo4d objects	formatData
Data from Darwin's finches	geospiza geospiza_raw
Node and Edge look-up functions	getEdge getEdge,phylo4-method getEdge-methods getNode getNode,phylo4-method
edgeLength methods	depthTips depthTips,phylo4-method depthTips,phylo4-methods edgeLength edgeLength,phylo4-method edgeLength<- edgeLength<-,phylo4,ANY-method edgeLength<-,phylo4-method hasEdgeLength hasEdgeLength,phylo4-method isUltrametric isUltrametric,phylo4-method nodeDepth nodeDepth,phylo4-method nodeHeight nodeHeight,phylo4-method sumEdgeLength sumEdgeLength,phylo4-method
Test trees for polytomies, inline nodes (singletons), or reticulation	hasPoly hasPoly,phylo4-method hasRetic hasRetic,phylo4-method hasSingle hasSingle,phylo4-method
Tests for presence of data associated with trees stored as phylo4d objects	hasNodeData hasNodeData,phylo4d-method hasNodeData-methods hasTipData hasTipData,phylo4d-method hasTipData-method,phylo4d-method nData nData,phylo4d-method
Create a 'phylo4', 'phylo4d' or 'data.frame' object from a NEXUS or a Newick file	Import Nexus and Newick files readNCL readNewick readNexus
Methods to test, access (and modify) the root of a phylo4 object.	isRooted isRooted,phylo4-method rootNode rootNode,phylo4-method rootNode<- rootNode<-,phylo4-method
MRCA	MRCA MRCA,phylo-method MRCA,phylo4-method
multiPhylo4 and extended classes	multiPhylo-class multiPhylo4-class multiPhylo4d-class tbind
nodeId methods	edgeId edgeId,phylo4-method nodeId nodeId,phylo4-method
nTips, nNodes, nEdges	nEdges nEdges,phylo4-method nNodes nNodes,phylo4-method nTips nTips,phylo-method nTips,phylo4-method
'Owls' data from ape	owls4
Constructor for pdata (phylogenetic data) class	check_pdata pdata
Class "pdata"	pdata-class ptypes [,pdata,ANY,ANY,ANY-method [,pdata-method [<-,pdata-method [[,pdata,ANY,ANY-method [[,pdata,ANY,missing-method [[,pdata-method [[<-,pdata-method
The phylo4 class	phylo4-class
Labels for phylo4/phylo4d objects	edgeLabels edgeLabels,phylo4-method edgeLabels<- edgeLabels<-,phylo4-method hasDuplicatedLabels hasDuplicatedLabels,phylo4,ANY-method hasDuplicatedLabels,phylo4-method hasEdgeLabels hasEdgeLabels,phylo4-method hasNodeLabels hasNodeLabels,phylo4-method labels labels,phylo4-method labels<- labels<-,phylo4-method nodeLabels nodeLabels,phylo4-method nodeLabels<- nodeLabels<-,phylo4-method phylo4-labels tipLabels tipLabels,phylo4-method tipLabels<- tipLabels<-,phylo4-method
Create a phylogenetic tree	nexml,phylo4-method phylo4 phylo4,matrix-method phylo4,nexml-method phylo4,phylo-method phylo4-methods phylo4_orderings
phylo4d class	phylo4d-class
Combine a phylogenetic tree with data	nexml,phylo4d-method phylo4d phylo4d,matrix,matrix-method phylo4d,matrix-method phylo4d,nexml-method phylo4d,phylo,phylo-method phylo4d,phylo-method phylo4d,phylo4,phylo4-method phylo4d,phylo4-method phylo4d,phylo4d,phylo4d-method phylo4d,phylo4d-method phylo4d-methods
Set or return options of phylobase	phylobase.options
Bubble plots for phylo4d objects	phylobubbles
matrix classes for phylobase	as_phylo4vcov phylo4vcov-class phylomat-class phylomat-setAs setAs,phylo,phylo4vcov-method setAs,phylo4vcov,phylo4-method
Calculate node x and y coordinates	phyloXXYY
Plot a phylo4 object	plotOneTree
print a phylogeny	head head,phylo4-method names names,phylo4-method print print,phylo4-method show show,phylo4-method tail tail,phylo4-method
reordering trees within phylobase objects	reorder reorder,phylo4-method reorder-methods
Converting between phylo4/phylo4d and other phylogenetic tree formats	as as,nexml,phylo4-method as,nexml,phylo4d-method as,phylo,phylo4-method as,phylo,phylo4d-method as,phylo4,phylo-method as-method setAs setAs,phylo4,data.frame-method setAs,phylo4,phylog-method
shortestPath-methods	shortestPath shortestPath,phylo-method shortestPath,phylo4-method shortestPath-phylo shortestPath-phylo4
Methods for creating subsets of phylogenies	prune prune,phylo4-method prune,phylo4d-method subset subset,phylo4-method subset-methods [ [,phylo4,ANY,ANY,ANY-method [,phylo4,character,missing,missing-method [,phylo4,logical,missing,missing-method [,phylo4,missing,missing,missing-method [,phylo4,numeric,missing,missing-method [,phylo4d,ANY,character,missing-method [,phylo4d,ANY,logical,missing-method [,phylo4d,ANY,numeric,missing-method
Summary for phylo4/phylo4d objects	nodeType nodeType,phylo4-method summary summary,phylo4-method summary,phylo4d-method summary-methods
Retrieving or updating tip and node data in phylo4d objects	nodeData nodeData,phylo4d-method nodeData-method nodeData<- nodeData<-,phylo4d,ANY-method nodeData<-,phylo4d-method tdata tdata,phylo4d-method tdata<- tdata<-,phylo4d,ANY-method tdata<-,phylo4d-method tipData tipData,phylo4d-method tipData-method tipData<- tipData<-,phylo4d,ANY-method tipData<-,phylo4d-method
Plotting trees and associated data	tip.data.plot
Phylogeny plotting	plot plot,ANY,ANY-method plot,pdata,missing-method plot,phylo4,missing-method plot,phylo4-method treePlot treePlot,phylo4,phylo4d-method treePlot-method treePlot-methods