[Phylobase-commits] r894 - in tags: . phylobase-0.6.8 phylobase-0.6.8/R phylobase-0.6.8/src phylobase-0.6.8/src/ncl
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Mar 20 23:08:16 CET 2014
Author: francois
Date: 2014-03-20 23:08:16 +0100 (Thu, 20 Mar 2014)
New Revision: 894
Added:
tags/phylobase-0.6.8/
tags/phylobase-0.6.8/.Rbuildignore
tags/phylobase-0.6.8/DESCRIPTION
tags/phylobase-0.6.8/NAMESPACE
tags/phylobase-0.6.8/NEWS
tags/phylobase-0.6.8/R/RcppExports.R
tags/phylobase-0.6.8/R/class-phylomats.R
tags/phylobase-0.6.8/R/methods-phylo4.R
tags/phylobase-0.6.8/R/readNCL.R
tags/phylobase-0.6.8/R/treewalk.R
tags/phylobase-0.6.8/src/GetNCL.cpp
tags/phylobase-0.6.8/src/Makevars
tags/phylobase-0.6.8/src/Makevars.win
tags/phylobase-0.6.8/src/RcppExports.cpp
tags/phylobase-0.6.8/src/checkPhylo4.cpp
tags/phylobase-0.6.8/src/ncl/nxsassumptionsblock.h
Removed:
tags/phylobase-0.6.8/DESCRIPTION
tags/phylobase-0.6.8/NAMESPACE
tags/phylobase-0.6.8/NEWS
tags/phylobase-0.6.8/R/RcppExports.R
tags/phylobase-0.6.8/R/class-phylomats.R
tags/phylobase-0.6.8/R/methods-phylo4.R
tags/phylobase-0.6.8/R/readNCL.R
tags/phylobase-0.6.8/R/treewalk.R
tags/phylobase-0.6.8/src/GetNCL.cpp
tags/phylobase-0.6.8/src/Makevars
tags/phylobase-0.6.8/src/Makevars.win
tags/phylobase-0.6.8/src/RcppExports.cpp
tags/phylobase-0.6.8/src/checkPhylo4.cpp
tags/phylobase-0.6.8/src/ncl/nxsassumptionsblock.h
Log:
tagging the 0.6.8 CRAN release.
Copied: tags/phylobase-0.6.8/.Rbuildignore (from rev 893, pkg/.Rbuildignore)
===================================================================
--- tags/phylobase-0.6.8/.Rbuildignore (rev 0)
+++ tags/phylobase-0.6.8/.Rbuildignore 2014-03-20 22:08:16 UTC (rev 894)
@@ -0,0 +1,6 @@
+TAGS
+TODO
+cleanup
+^\.
+.?svn.?
+~$
Deleted: tags/phylobase-0.6.8/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2014-03-17 13:29:22 UTC (rev 880)
+++ tags/phylobase-0.6.8/DESCRIPTION 2014-03-20 22:08:16 UTC (rev 894)
@@ -1,51 +0,0 @@
-Package: phylobase
-Type: Package
-Title: Base package for phylogenetic structures and comparative data
-Version: 0.6.8
-Date: 2014-03-17
-Imports: ade4,
- ape (>= 3.0),
- Rcpp (>= 0.11.0),
- methods
-Depends:
- grid
-LinkingTo: Rcpp
-Suggests:
- MASS,
- testthat (>= 0.8.1),
- RUnit
-Author: 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)
-Maintainer: Francois Michonneau <francois.michonneau at gmail.com>
-Description: Provides a base S4 class for comparative methods, incorporating
- one or more trees and trait data
-License: GPL (>= 2)
-Collate:
- 'RcppExports.R'
- 'phylo4.R'
- 'checkdata.R'
- 'formatData.R'
- 'class-multiphylo4.R'
- 'class-oldclasses.R'
- 'class-phylo4.R'
- 'class-phylo4d.R'
- 'class-phylomats.R'
- 'methods-multiphylo4.R'
- 'methods-oldclasses.R'
- 'methods-phylo4.R'
- 'methods-phylo4d.R'
- 'setAs-Methods.R'
- 'pdata.R'
- 'subset.R'
- 'phylobase-package.R'
- 'phylobase.options.R'
- 'prune.R'
- 'treePlot.R'
- 'treestruc.R'
- 'treewalk.R'
- 'readNCL.R'
- 'tbind.R'
- 'zzz.R'
-URL: http://phylobase.R-forge.R-project.org
Copied: tags/phylobase-0.6.8/DESCRIPTION (from rev 892, pkg/DESCRIPTION)
===================================================================
--- tags/phylobase-0.6.8/DESCRIPTION (rev 0)
+++ tags/phylobase-0.6.8/DESCRIPTION 2014-03-20 22:08:16 UTC (rev 894)
@@ -0,0 +1,52 @@
+Package: phylobase
+Type: Package
+Title: Base package for phylogenetic structures and comparative data
+Version: 0.6.8
+Date: 2014-03-20
+Imports:
+ ade4,
+ ape (>= 3.0),
+ Rcpp (>= 0.11.0),
+ methods
+Depends:
+ grid
+LinkingTo: Rcpp
+Suggests:
+ MASS,
+ testthat (>= 0.8.1),
+ RUnit
+Author: 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)
+Maintainer: Francois Michonneau <francois.michonneau at gmail.com>
+Description: Provides a base S4 class for comparative methods, incorporating
+ one or more trees and trait data
+License: GPL (>= 2)
+Collate:
+ 'RcppExports.R'
+ 'phylo4.R'
+ 'checkdata.R'
+ 'formatData.R'
+ 'class-multiphylo4.R'
+ 'class-oldclasses.R'
+ 'class-phylo4.R'
+ 'class-phylo4d.R'
+ 'class-phylomats.R'
+ 'methods-multiphylo4.R'
+ 'methods-oldclasses.R'
+ 'methods-phylo4.R'
+ 'methods-phylo4d.R'
+ 'setAs-Methods.R'
+ 'pdata.R'
+ 'subset.R'
+ 'phylobase-package.R'
+ 'phylobase.options.R'
+ 'prune.R'
+ 'treePlot.R'
+ 'treestruc.R'
+ 'treewalk.R'
+ 'readNCL.R'
+ 'tbind.R'
+ 'zzz.R'
+URL: http://phylobase.R-forge.R-project.org
Deleted: tags/phylobase-0.6.8/NAMESPACE
===================================================================
--- pkg/NAMESPACE 2014-03-17 13:29:22 UTC (rev 880)
+++ tags/phylobase-0.6.8/NAMESPACE 2014-03-20 22:08:16 UTC (rev 894)
@@ -1,119 +0,0 @@
-# ----------------------------------------------------------------------
-
-useDynLib(phylobase)
-
-#----------------------------------------------------------------------
-
-import(methods)
-import(ape)
-import(Rcpp)
-
-importFrom(graphics, plot)
-importFrom(stats, reorder)
-importFrom(utils, head, tail)
-importFrom(ade4, newick2phylog)
-
-#----------------------------------------------------------------------
-
-exportClasses(phylo4, phylo4d, multiPhylo4, multiPhylo4d)
-
-#----------------------------------------------------------------------
-
-# utility methods
-exportMethods(print, head, tail, reorder, plot, summary)
-
-# tree constructor methods
-exportMethods(phylo4, phylo4d)
-
-# counting methods
-exportMethods(nTips, nNodes, nEdges, depthTips)
-
-# edge methods
-exportMethods(edges, edgeId, hasEdgeLength, edgeLength, "edgeLength<-",
- sumEdgeLength, edgeOrder)
-
-# root methods
-exportMethods(isRooted, rootNode, "rootNode<-")
-#export(rootEdge) # no methods defined yet?
-
-# node methods
-exportMethods(nodeId, nodeType, nodeDepth)
-
-# tree properties methods
-exportMethods(isUltrametric)
-
-# tree data methods
-exportMethods(tdata, "tdata<-", tipData, "tipData<-", nodeData,
- "nodeData<-", hasTipData, hasNodeData, addData, nData)
-
-# subset methods
-exportMethods(subset, prune, "[")
-
-# pdata methods
-exportMethods("[<-", "[[", "[[<-")
-
-# label methods
-exportMethods(labels, "labels<-", nodeLabels, "nodeLabels<-",
- tipLabels, "tipLabels<-", edgeLabels, "edgeLabels<-",
- hasNodeLabels, hasEdgeLabels, hasDuplicatedLabels)
-
-#----------------------------------------------------------------------
-
-# tree structure functions
-export(hasPoly, hasSingle, hasRetic)
-
-# treewalk functions
-export(getNode, ancestor, children, descendants, siblings, ancestors,
- MRCA, shortestPath, getEdge)
-
-# Import functions
-export(readNexus)
-export(readNewick)
-export(readNCL)
-
-# pdata functions
-export(pdata, check_pdata)
-
-# plotting functions
-export(treePlot, plotOneTree, tip.data.plot)
-export(phyloXXYY, phylobubbles)
-
-# misc functions
-export(extractTree, tbind)
-export(checkPhylo4, checkTree, checkPhylo4Data, formatData)
-export(as_phylo4vcov)
-export(printphylo4)
-
-#----------------------------------------------------------------------
-
-# misc objects
-export(phylo4_orderings)
-
-## options
-export(phylobase.options)
-
-
-
-## commented out in source code, probably should be omitted here
-#export(phyloStripchart)
-#export(internEdges, terminEdges, isPoly)
-
-## presumably these should remain hidden
-##export(.createLabels, .createEdge, .phylo4Data, orderIndex, .genlab,
-## .chnumsort, .phylo4ToDataFrame, .bubLegendGrob)
-## hidden: drawDetails.bubLegend)
-
-## recently removed:
-## tree.plot
-## segs
-## checkData
-## attachData
-## orderIndex
-
-#----------------------------------------------------------------------
-## For reference, quick & dirty UNIX-y commandline statements to pull
-## out methods and functions from package code; use in pkg/R/ dir:
-# grep "^ *setMethod" *.R | sed 's/setMethod(//' | sed 's/.*:["]\([^,]*\)["].*/\1/' | sort | uniq
-# grep "^ *setReplaceMethod" *.R | sed 's/setReplaceMethod(//' | sed 's/.*:["]\([^,]*\)["].*/\1/' | sort | uniq
-# grep "^[^ ].*<- *function *(" *.R | sed 's/.*R://'
-
Copied: tags/phylobase-0.6.8/NAMESPACE (from rev 886, pkg/NAMESPACE)
===================================================================
--- tags/phylobase-0.6.8/NAMESPACE (rev 0)
+++ tags/phylobase-0.6.8/NAMESPACE 2014-03-20 22:08:16 UTC (rev 894)
@@ -0,0 +1,119 @@
+# ----------------------------------------------------------------------
+
+useDynLib(phylobase)
+
+#----------------------------------------------------------------------
+
+import(methods)
+import(ape)
+
+importFrom(Rcpp, evalCpp)
+importFrom(graphics, plot)
+importFrom(stats, reorder)
+importFrom(utils, head, tail)
+importFrom(ade4, newick2phylog)
+
+#----------------------------------------------------------------------
+
+exportClasses(phylo4, phylo4d, multiPhylo4, multiPhylo4d)
+
+#----------------------------------------------------------------------
+
+# utility methods
+exportMethods(print, head, tail, reorder, plot, summary)
+
+# tree constructor methods
+exportMethods(phylo4, phylo4d)
+
+# counting methods
+exportMethods(nTips, nNodes, nEdges, depthTips)
+
+# edge methods
+exportMethods(edges, edgeId, hasEdgeLength, edgeLength, "edgeLength<-",
+ sumEdgeLength, edgeOrder)
+
+# root methods
+exportMethods(isRooted, rootNode, "rootNode<-")
+#export(rootEdge) # no methods defined yet?
+
+# node methods
+exportMethods(nodeId, nodeType, nodeDepth)
+
+# tree properties methods
+exportMethods(isUltrametric)
+
+# tree data methods
+exportMethods(tdata, "tdata<-", tipData, "tipData<-", nodeData,
+ "nodeData<-", hasTipData, hasNodeData, addData, nData)
+
+# subset methods
+exportMethods(subset, prune, "[")
+
+# pdata methods
+exportMethods("[<-", "[[", "[[<-")
+
+# label methods
+exportMethods(labels, "labels<-", nodeLabels, "nodeLabels<-",
+ tipLabels, "tipLabels<-", edgeLabels, "edgeLabels<-",
+ hasNodeLabels, hasEdgeLabels, hasDuplicatedLabels)
+
+#----------------------------------------------------------------------
+
+# tree structure functions
+export(hasPoly, hasSingle, hasRetic)
+
+# treewalk functions
+export(getNode, ancestor, children, descendants, siblings, ancestors,
+ MRCA, shortestPath, getEdge)
+
+# Import functions
+export(readNexus)
+export(readNewick)
+export(readNCL)
+
+# pdata functions
+export(pdata, check_pdata)
+
+# plotting functions
+export(treePlot, plotOneTree, tip.data.plot)
+export(phyloXXYY, phylobubbles)
+
+# misc functions
+export(extractTree, tbind)
+export(checkPhylo4, checkTree, checkPhylo4Data, formatData)
+export(as_phylo4vcov)
+export(printphylo4)
+
+#----------------------------------------------------------------------
+
+# misc objects
+export(phylo4_orderings)
+
+## options
+export(phylobase.options)
+
+
+
+## commented out in source code, probably should be omitted here
+#export(phyloStripchart)
+#export(internEdges, terminEdges, isPoly)
+
+## presumably these should remain hidden
+##export(.createLabels, .createEdge, .phylo4Data, orderIndex, .genlab,
+## .chnumsort, .phylo4ToDataFrame, .bubLegendGrob)
+## hidden: drawDetails.bubLegend)
+
+## recently removed:
+## tree.plot
+## segs
+## checkData
+## attachData
+## orderIndex
+
+#----------------------------------------------------------------------
+## For reference, quick & dirty UNIX-y commandline statements to pull
+## out methods and functions from package code; use in pkg/R/ dir:
+# grep "^ *setMethod" *.R | sed 's/setMethod(//' | sed 's/.*:["]\([^,]*\)["].*/\1/' | sort | uniq
+# grep "^ *setReplaceMethod" *.R | sed 's/setReplaceMethod(//' | sed 's/.*:["]\([^,]*\)["].*/\1/' | sort | uniq
+# grep "^[^ ].*<- *function *(" *.R | sed 's/.*R://'
+
Deleted: tags/phylobase-0.6.8/NEWS
===================================================================
--- pkg/NEWS 2014-03-17 13:29:22 UTC (rev 880)
+++ tags/phylobase-0.6.8/NEWS 2014-03-20 22:08:16 UTC (rev 894)
@@ -1,230 +0,0 @@
-
-
-
- *************************************************
- * *
- * 0.6 SERIES NEWS *
- * *
- *************************************************
-
- 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()
-
-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.
-
-
- *************************************************
- * *
- * 0.5 SERIES NEWS *
- * *
- *************************************************
-
- 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.
Copied: tags/phylobase-0.6.8/NEWS (from rev 888, pkg/NEWS)
===================================================================
--- tags/phylobase-0.6.8/NEWS (rev 0)
+++ tags/phylobase-0.6.8/NEWS 2014-03-20 22:08:16 UTC (rev 894)
@@ -0,0 +1,249 @@
+
+
+
+ *************************************************
+ * *
+ * 0.6 SERIES NEWS *
+ * *
+ *************************************************
+
+ 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()
+
+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.
+
+
+ *************************************************
+ * *
+ * 0.5 SERIES NEWS *
+ * *
+ *************************************************
+
+ 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.
Deleted: tags/phylobase-0.6.8/R/RcppExports.R
===================================================================
--- pkg/R/RcppExports.R 2014-03-17 13:29:22 UTC (rev 880)
+++ tags/phylobase-0.6.8/R/RcppExports.R 2014-03-20 22:08:16 UTC (rev 894)
@@ -1,79 +0,0 @@
-# This file was generated by Rcpp::compileAttributes
-# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
-
-isLabelName <- function(lblToCheck, lbl) {
- .Call('phylobase_isLabelName', PACKAGE = 'phylobase', lblToCheck, lbl)
-}
-
-nRoots <- function(ances) {
- .Call('phylobase_nRoots', PACKAGE = 'phylobase', ances)
-}
-
-tabulateTips <- function(ances) {
- .Call('phylobase_tabulateTips', PACKAGE = 'phylobase', ances)
-}
-
-nTipsSafe <- function(ances) {
- .Call('phylobase_nTipsSafe', PACKAGE = 'phylobase', ances)
-}
-
-nTipsFastCpp <- function(ances) {
- .Call('phylobase_nTipsFastCpp', PACKAGE = 'phylobase', ances)
-}
-
-hasSingleton <- function(ances) {
- .Call('phylobase_hasSingleton', PACKAGE = 'phylobase', ances)
-}
-
-hasPolytomy <- function(ances) {
- .Call('phylobase_hasPolytomy', PACKAGE = 'phylobase', ances)
-}
-
-tipsSafe <- function(ances, desc) {
- .Call('phylobase_tipsSafe', PACKAGE = 'phylobase', ances, desc)
-}
-
-tipsFast <- function(ances) {
- .Call('phylobase_tipsFast', PACKAGE = 'phylobase', ances)
-}
-
-getAllNodesSafe <- function(edge) {
- .Call('phylobase_getAllNodesSafe', PACKAGE = 'phylobase', edge)
-}
-
-getAllNodesFast <- function(edge, rooted) {
- .Call('phylobase_getAllNodesFast', PACKAGE = 'phylobase', edge, rooted)
-}
-
-testEqInt <- function(x, y) {
- .Call('phylobase_testEqInt', PACKAGE = 'phylobase', x, y)
-}
-
-all_naC <- function(x) {
- .Call('phylobase_all_naC', PACKAGE = 'phylobase', x)
-}
-
-any_naC <- function(x) {
- .Call('phylobase_any_naC', PACKAGE = 'phylobase', x)
-}
-
-nb_naC <- function(x) {
- .Call('phylobase_nb_naC', PACKAGE = 'phylobase', x)
-}
-
-getRange <- function(x, na_rm) {
- .Call('phylobase_getRange', PACKAGE = 'phylobase', x, na_rm)
-}
-
-hasDuplicatedLabelsCpp <- function(label) {
- .Call('phylobase_hasDuplicatedLabelsCpp', PACKAGE = 'phylobase', label)
-}
-
-edgeIdCpp <- function(edge, type) {
- .Call('phylobase_edgeIdCpp', PACKAGE = 'phylobase', edge, type)
-}
-
-checkTreeCpp <- function(obj, opts) {
- .Call('phylobase_checkTreeCpp', PACKAGE = 'phylobase', obj, opts)
-}
-
Copied: tags/phylobase-0.6.8/R/RcppExports.R (from rev 887, pkg/R/RcppExports.R)
===================================================================
--- tags/phylobase-0.6.8/R/RcppExports.R (rev 0)
+++ tags/phylobase-0.6.8/R/RcppExports.R 2014-03-20 22:08:16 UTC (rev 894)
@@ -0,0 +1,83 @@
+# This file was generated by Rcpp::compileAttributes
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+isLabelName <- function(lblToCheck, lbl) {
+ .Call('phylobase_isLabelName', PACKAGE = 'phylobase', lblToCheck, lbl)
+}
+
+nRoots <- function(ances) {
+ .Call('phylobase_nRoots', PACKAGE = 'phylobase', ances)
+}
+
+tabulateTips <- function(ances) {
+ .Call('phylobase_tabulateTips', PACKAGE = 'phylobase', ances)
+}
+
+nTipsSafe <- function(ances) {
+ .Call('phylobase_nTipsSafe', PACKAGE = 'phylobase', ances)
+}
+
+nTipsFastCpp <- function(ances) {
+ .Call('phylobase_nTipsFastCpp', PACKAGE = 'phylobase', ances)
+}
+
+hasSingleton <- function(ances) {
+ .Call('phylobase_hasSingleton', PACKAGE = 'phylobase', ances)
+}
+
+hasPolytomy <- function(ances) {
+ .Call('phylobase_hasPolytomy', PACKAGE = 'phylobase', ances)
+}
+
+tipsSafe <- function(ances, desc) {
+ .Call('phylobase_tipsSafe', PACKAGE = 'phylobase', ances, desc)
+}
+
+tipsFast <- function(ances) {
+ .Call('phylobase_tipsFast', PACKAGE = 'phylobase', ances)
+}
+
+getAllNodesSafe <- function(edge) {
+ .Call('phylobase_getAllNodesSafe', PACKAGE = 'phylobase', edge)
+}
+
+getAllNodesFast <- function(edge, rooted) {
+ .Call('phylobase_getAllNodesFast', PACKAGE = 'phylobase', edge, rooted)
+}
+
+testEqInt <- function(x, y) {
+ .Call('phylobase_testEqInt', PACKAGE = 'phylobase', x, y)
+}
+
+all_naC <- function(x) {
+ .Call('phylobase_all_naC', PACKAGE = 'phylobase', x)
+}
+
+any_naC <- function(x) {
+ .Call('phylobase_any_naC', PACKAGE = 'phylobase', x)
+}
+
+nb_naC <- function(x) {
+ .Call('phylobase_nb_naC', PACKAGE = 'phylobase', x)
+}
+
+getRange <- function(x, na_rm) {
+ .Call('phylobase_getRange', PACKAGE = 'phylobase', x, na_rm)
+}
+
+hasDuplicatedLabelsCpp <- function(label) {
+ .Call('phylobase_hasDuplicatedLabelsCpp', PACKAGE = 'phylobase', label)
+}
+
+edgeIdCpp <- function(edge, type) {
+ .Call('phylobase_edgeIdCpp', PACKAGE = 'phylobase', edge, type)
+}
+
+checkTreeCpp <- function(obj, opts) {
+ .Call('phylobase_checkTreeCpp', PACKAGE = 'phylobase', obj, opts)
+}
+
+GetNCL <- function(params, paramsVecR) {
+ .Call('phylobase_GetNCL', PACKAGE = 'phylobase', params, paramsVecR)
+}
+
Deleted: tags/phylobase-0.6.8/R/class-phylomats.R
===================================================================
--- pkg/R/class-phylomats.R 2014-03-17 13:29:22 UTC (rev 880)
+++ tags/phylobase-0.6.8/R/class-phylomats.R 2014-03-20 22:08:16 UTC (rev 894)
@@ -1,129 +0,0 @@
-
-#' matrix classes for phylobase
-#'
-#' Classes representing phylogenies as matrices
-#'
-#'
-#' @name phylomat-class
-#' @aliases phylo4vcov-class as_phylo4vcov
-#' @docType class
-#' @param from a \code{phylo4} object
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/phylobase -r 894
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