Base Package for Phylogenetic Structures and Comparative Data

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


News

CHANGES in phylobase VERSION 0.8.6

  • CRAN maintenance release following updates to RNeXML.

CHANGES in phylobase VERSION 0.8.4

  • CRAN maintenance release

CHANGES in phylobase VERSION 0.8.2

  • Fix typo in examples of phylo4d methods.

CHANGES IN phylobase VERSION 0.8.0

New features

  • Initial basic support for converting RNeXML objects in phylo4 and phylo4d format.

  • New methods: internalEdges(), terminalEdges()

  • descendants() has now a "ALL" argument to include self in results

  • New method: nodeHeight() provides a consistent and comprehensive way of calculating the distance between a node and either the root or the tips. (fix #3)

  • The replacement methods for labels, tipLabels, nodeLabels, edgeLabels now accept NA or NULL to remove labels (fix #2)

Major changes

  • readNexus and readNewick now internally use the package rncl to parse files. They also use a different approach to reconstruct the edge matrix. These changes make file parsing faster. Objects created with this new approach may not exactly be identical to those created in previous versions as node numbering might differ, they should however be fully compatible with each others.

  • readNexus and readNewick can now parse tree files with trees containing a subset of the taxa listed in the TAXA Block.

  • Source code for the package is hosted on GitHub at https://github.com/fmichonneau/phylobase

Minor changes

  • All tests done with testthat

  • rootNode returns the rootNode using the same format as getNode().

  • All documentation is in Roxygen format

  • hasPoly, hasRetic, hasSingle are now methods instead of functions.

Deprecated functions

  • nodeDepth and depthTips are now deprecated and are replaced by nodeHeight

Bug fixes

  • Fix bug: NA in labels were considered duplicated by checkPhylo4().

  • Fix bug #605 (R-forge) -- treePlot subsets numeric data for plotting.

  • Fix bug #4: descendants() behave like ancestors() when provided with a vector of nodes and is consistent across all arguments.

CHANGES IN phylobase VERSION 0.6.8

  • Not many user-visible changes, most are related to improving speeds during test of object validation (most tests done in C++) and to getNode that is used by many functions.

  • Changes to package structure to make it compatible with devtools (switching testing to testthat -- partial at this stage) and docs to roxygen format (partial at this stage).

  • Changes to package structure to comply with new Rcpp standards

CHANGES IN phylobase VERSION 0.6.5

  • Updates from cout/cerr to Rcpp::Rcout/Rcerr

  • Comments in Nexus tree strings are being removed before being processed by readNCL

CHANGES IN phylobase VERSION 0.6.3

  • Fixed bugs in getNode in cases where labels included regexpr metacharacters and when a tip was labelled 0

  • New methods: depthTips, nodeDepth and isUltrametric

CHANGES IN phylobase VERSION 0.6.2

  • Improve handling of errors returned by NCL (NxsException)

  • Fix bug in case state labels are missing from the NEXUS file

  • Upgrade to NCL 2.1.14

CHANGES IN phylobase VERSION 0.6.1

  • Fix bugs that prevented building on Windows 64-bit systems

CHANGES IN phylobase VERSION 0.6

MAJOR CHANGES

  • Updated to the Nexus Class Library (NCL) 2.1.12.

  • Changed the way NCL is built during the installation process.

  • Complete rewrite of the function readNexus which brings many new functionalities.

  • Nodes labels do not have to be unique.

NEW FEATURES

  • In readNexus, the option return.labels gives the state labels of the characters.

  • It is now possible to import several types of data blocks in a single NEXUS file with readNexus.

  • The function phylobase.options() provides global options to control the behavior of the phylo4/phylo4d validator.

  • The new method hasDuplicatedLabels() indicates whether any node labels are duplicated.

  • The new method nData() returns the number of datasets associated with a tree.

  • The column that contains the labels can now be specified by its name in the function formatData()

MINOR CHANGES

  • The function getNode() has been modified to allow node matching in the case of non-unique labels.

  • Many new unit tests.

BUG FIXES

  • Far too many to document. See the SVN log for details.

KNOWN ISSUES

  • Unrooted trees are not supported by all functions, e.g. plot() and reorder().

  • Factors are not supported by the default plotting method.

CHANGES IN phylobase VERSION 0.5

MAJOR CHANGES

  • A var-cov matrix tree class, phylo4vcov, and methods for converting to and from other classes now exists.

  • Replaced separate the tip.label and node.label slots with a unified label slot in the phylo4 class definition.

  • Replaced separate the tip.data and node.data into a single data slot in the phylo4d class definition.

  • The phylo4 class grew a annotate slot.

  • The phylo4d class grew a metadata slot.

  • Added an order slot to the phylo4 class definition and updated as() methods to assign the proper order (if possible) when converting between ape and phylobase tree formats.

  • The Nnode slot was removed from the phylo4 class definition.

  • An explicit root edge has been added to the edge matrix with 0 as the ancestor and nTips(phy) + 1 as the rood node.

  • The edgeLabels() and edgeLength() accessors now return vectors with named elements in the same order as rows of the edge matrix, even when some/all values are missing.

  • The labels() accessor and nodeID() methods now always return labels in ascending order of node ID

  • Many function and argument names and defaults have been changed to make them more consistent most functions follow the getNode() pattern.

  • The plotting functions have been replaced (see below).

  • Now, data are matched against node numbers instead of node labels.

  • Tip and internal node labels have now internal names that are character strings of the node number they correspond to. Thus it is possible to store labels in any order and assignment of labels more robust.

  • We now use the RUnit package (not required for normal use) for adding unit tests. Adding unit tests to inst/unitTests/ is now preferred over the tests/ directory.

  • Numerous changes to pruning and tree subsetting code. It is considerably more robust and no longer relies on calls to APE.

NEW FEATURES

  • Added a function nodeType() for identifying whether a node is root, tip or internal.

  • Changed nodeNumbers to nodeId() and extended it abilities.

  • Added method reorder() for converting edge matrices into preorder or postorder.

  • Added the edgeOrder accessor to get the order of a phylobase object.

  • Added a package help file accessible from ?phylobase.

  • Added labels()<- for assigning labels.

  • Added edgeLength()<- for assigning edgeLengths.

  • Added a phylo4() method for importing APE phylo objects.

  • Added a hasTipData() method.

  • Added a edgeId() method.

  • Created the addData() method for adding data to phylo4 objects.

  • Added tipData and nodeData getter/setter methods

  • If all node.labels are numerical values, they are automatically converted as data. Useful when importing consensus tree from MrBayes.

  • It is now possible to print tree objects in edge order using the edgeOrder argument in printphylo4().

  • reorder(), descendants(), ancestors(), and portions of the plotting code have been recoded in C to improve performance.

  • Added a developer vignette to document and guide development of the phylobase package.

  • The previous plotting functions, based on base graphics, have been replaced with function based on the grid graphics device.

  • A S4 generic plot() function, calling treePlot() has been added it dispatches a plotting function based on object class and arguments.

  • Plots using grid based code can be inserted at the tree tips using the tip.plot.fun argument in plot()

  • The getNode() method has been enhanced to allow matching against specific node types, and if the requested node is missing, all nodes of specified type are returned.

  • Changed getEdge() to allow no node argument, which returns all edges appropriate for the given type.

CHANGES

  • Node labels are, if not supplied, a vector of NA.

  • printphylo() is now deprecated, print() and summary() now alsow work on empty objects.

  • phylo4() is now and S4 generic with signature "matrix".

  • phylobase now uses a NAMESPACE file.

  • Legacy plotting code (0.4) can be found in the SVN repo tags directory.

  • The tdata default "type" argument changed to 'all'.

  • Row names now stored internally as numeric, not character.

BUG FIXES

  • Far too many to document. See the SVN log for details.

KNOWN ISSUES

  • Unrooted trees are not supported by all functions, e.g. plot() and reorder().

  • Factors are not supported by the default plotting method.

  • The Nexus Class Library is build for the system default ARCH which may or may not be the architecture that R and the rest of the package is built with. If this occurs the package will fail to load.

  • Unique labels are required for internal nodes, this behavior will be changed in the future.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("phylobase")

0.8.6 by Francois Michonneau, 2 months ago


https://github.com/fmichonneau/phylobase


Report a bug at https://github.com/fmichonneau/phylobase/issues


Browse source code at https://github.com/cran/phylobase


Authors: R Hackathon et al. (alphabetically: Ben Bolker , Marguerite Butler , Peter Cowan , Damien de Vienne , Dirk Eddelbuettel , Mark Holder , Thibaut Jombart , Steve Kembel , Francois Michonneau , David Orme , Brian O'Meara , Emmanuel Paradis , Jim Regetz , Derrick Zwickl)


Documentation:   PDF Manual  


Task views: Phylogenetics, Especially Comparative Methods


GPL (>= 2) license


Imports ade4, ape, Rcpp, rncl, grid, methods, stats, RNeXML

Suggests MASS, testthat, knitr

Linking to Rcpp


Imported by BMhyb, BMhyd, PCPS, SigTree, adephylo, phyext2, phyloTop, phylocanvas, phylosignal.

Depended on by adiv.

Suggested by expands, rotl.


See at CRAN