Package: phylobase 0.8.12
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:
phylobase_0.8.12.tar.gz
phylobase_0.8.12.zip(r-4.5)phylobase_0.8.12.zip(r-4.4)phylobase_0.8.12.zip(r-4.3)
phylobase_0.8.12.tgz(r-4.4-x86_64)phylobase_0.8.12.tgz(r-4.4-arm64)phylobase_0.8.12.tgz(r-4.3-x86_64)phylobase_0.8.12.tgz(r-4.3-arm64)
phylobase_0.8.12.tar.gz(r-4.5-noble)phylobase_0.8.12.tar.gz(r-4.4-noble)
phylobase_0.8.12.tgz(r-4.4-emscripten)phylobase_0.8.12.tgz(r-4.3-emscripten)
phylobase.pdf |phylobase.html✨
phylobase/json (API)
NEWS
| # Install 'phylobase' in R: |
| install.packages('phylobase', repos = c('https://fmichonneau.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/fmichonneau/phylobase/issues
- geospiza - Data from Darwin's finches
- geospiza_raw - Data from Darwin's finches
- owls4 - 'Owls' data from ape
Last updated 10 months agofrom:5eecded489. Checks:OK: 9. Indexed: yes.
| 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:[addDataancestorancestorscheckPhylo4childrendepthTipsdescendantsedgeIdedgeLabelsedgeLabels<-edgeLengthedgeLength<-edgeOrderedgesextractTreegetEdgegetNodehasDuplicatedLabelshasEdgeLabelshasEdgeLengthhasNodeDatahasNodeLabelshasPolyhasRetichasSinglehasTipDataheadinternalEdgesisRootedisUltrametriclabelslabels<-MRCAnamesnDatanEdgesnNodesnodeDatanodeData<-nodeDepthnodeHeightnodeIdnodeLabelsnodeLabels<-nodeTypenTipsphylo4phylo4dphylobase.optionsphylobubblesphyloXXYYplotplotOneTreeprintprunereadNCLreadNewickreadNexusreorderrootNoderootNode<-shortestPathshowsiblingssubsetsumEdgeLengthsummarytailtdatatdata<-terminalEdgestip.data.plottipDatatipData<-tipLabelstipLabels<-treePlot
Dependencies:ade4apeaskpassclicpp11crayoncurldigestdplyrfansigenericsgluehmshttrjsonlitelatticelifecyclemagrittrMASSmimenlmeopensslpillarpixmappkgconfigplyrprettyunitsprogresspurrrR6RcppRcppArmadilloreshape2rlangrnclRNeXMLspstringistringrsystibbletidyrtidyselectutf8uuidvctrswithrXMLxml2
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 |
