phylobase v0.8.10
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Base Package for Phylogenetic Structures and Comparative Data
Provides a base S4 class for comparative methods, incorporating
one or more trees and trait data.
Functions in phylobase
| Name | Description | |
| hasEdgeLength | edgeLength methods | |
| nodeId | nodeId methods | |
| setAs | Converting between phylo4/phylo4d and other phylogenetic tree formats | |
| nTips | nTips, nNodes, nEdges | |
| phylobubbles | Bubble plots for phylo4d objects | |
| geospiza | Data from Darwin's finches | |
| phylobase.options | Set or return options of phylobase | |
| addData | Adding data to a phylo4 or a phylo4d object | |
| edges | Edges accessors | |
| shortestPath | shortestPath-methods | |
| ancestor | Tree traversal and utility functions | |
| multiPhylo-class | multiPhylo4 and extended classes | |
| getNode | Node and Edge look-up functions | |
| phylo4-methods | Create a phylogenetic tree | |
| phylo4-class | The phylo4 class | |
| pdata | Constructor for pdata (phylogenetic data) class | |
| print a phylogeny | ||
| owls4 | 'Owls' data from ape | |
| phyloXXYY | Calculate node x and y coordinates | |
| phylo4d-class | phylo4d class | |
| pdata-class | Class "pdata" | |
| Import Nexus and Newick files | Create a phylo4, phylo4d or data.frame object from a NEXUS or a Newick file | |
| phylo4d-methods | Combine a phylogenetic tree with data | |
| checkPhylo4 | Validity checking for phylo4 objects | |
| hasTipData | Tests for presence of data associated with trees stored as phylo4d objects | |
| tdata | Retrieving or updating tip and node data in phylo4d objects | |
| subset-methods | Methods for creating subsets of phylogenies | |
| hasSingle | Test trees for polytomies, inline nodes (singletons), or reticulation | |
| plotOneTree | Plot a phylo4 object | |
| tip.data.plot | Plotting trees and associated data | |
| isRooted | Methods to test, access (and modify) the root of a phylo4 object. | |
| summary-methods | Summary for phylo4/phylo4d objects | |
| treePlot-methods | Phylogeny plotting | |
| phylobase-package | Utilities and Tools for Phylogenetics | |
| phylomat-class | matrix classes for phylobase | |
| reorder-methods | reordering trees within phylobase objects | |
| formatData | Format data for use in phylo4d objects | |
| MRCA | MRCA | |
| phylo4-labels | Labels for phylo4/phylo4d objects | |
| extractTree | Get tree from tree+data object | |
| No Results! | ||
Vignettes of phylobase
| Name | ||
| phylobase.Rnw | ||
| No Results! | ||
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Details
| Type | Package |
| LinkingTo | Rcpp |
| License | GPL (>= 2) |
| URL | https://github.com/fmichonneau/phylobase |
| BugReports | https://github.com/fmichonneau/phylobase/issues |
| LazyData | true |
| Collate | 'oldclasses-class.R' 'internal-constructors.R' 'phylo4-methods.R' 'RcppExports.R' 'checkdata.R' 'phylo4-class.R' 'getNode-methods.R' 'formatData.R' 'phylo4d-class.R' 'phylo4d-methods.R' 'MRCA-methods.R' 'addData-methods.R' 'ancestors.R' 'phylo4-accessors.R' 'root-methods.R' 'nodeId-methods.R' 'edgeLength-methods.R' 'setAs-methods.R' 'extractTree.R' 'labels-methods.R' 'multiphylo4-class.R' 'pdata.R' 'phylo4d-accessors.R' 'phylobase-package.R' 'phylobase.options.R' 'phylomats-class.R' 'print-methods.R' 'readNCL.R' 'reorder-methods.R' 'shortestPath-methods.R' 'subset-methods.R' 'summary-methods.R' 'tbind.R' 'tdata-methods.R' 'treePlot.R' 'treestruc.R' 'zzz.R' |
| VignetteBuilder | knitr |
| RoxygenNote | 7.0.2.9000 |
| Encoding | UTF-8 |
| NeedsCompilation | yes |
| Packaged | 2020-03-01 07:30:03 UTC; francois |
| Repository | CRAN |
| Date/Publication | 2020-03-01 08:00:06 UTC |
| imports | ade4 , ape (>= 3.0) , grid , methods , Rcpp (>= 0.11.0) , rncl (>= 0.6.0) , RNeXML , stats |
| suggests | knitr , MASS , testthat (>= 0.8.1) |
| Contributors | Marguerite Butler, Jim Regetz, Mark Holder, Dirk Eddelbuettel, Emmanuel Paradis, Damien Vienne, David Orme, R et al, Peter Cowan, Thibaut Jombart, Steve Kembel, Francois Michonneau, Brian O'Meara, Derrick Zwickl) |
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