[Phylobase-commits] r701 - in tags: . phylobase-0.5 phylobase-0.5/inst/doc

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sat Oct 31 02:46:01 CET 2009 

Author: pdc
Date: 2009-10-31 02:46:01 +0100 (Sat, 31 Oct 2009)
New Revision: 701

Added:
   tags/phylobase-0.5/
   tags/phylobase-0.5/DESCRIPTION
   tags/phylobase-0.5/NEWS
   tags/phylobase-0.5/inst/doc/developer.pdf
   tags/phylobase-0.5/inst/doc/phylobase.pdf
Removed:
   tags/phylobase-0.5/DESCRIPTION
   tags/phylobase-0.5/inst/doc/developer.pdf
   tags/phylobase-0.5/inst/doc/phylobase.pdf
Log:
Add tag for phylobase 0.5

Copied: tags/phylobase-0.5 (from rev 697, pkg)

Deleted: tags/phylobase-0.5/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2009-10-27 14:44:21 UTC (rev 697)
+++ tags/phylobase-0.5/DESCRIPTION	2009-10-31 01:46:01 UTC (rev 701)
@@ -1,13 +0,0 @@
-Package: phylobase
-Type: Package
-Title: Base package for phylogenetic structures and comparative data
-Version: 0.4.1
-Date: 2009-04-21
-Depends: methods, grid, ape(>= 2.1)
-Suggests: ade4, MASS
-Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler, Peter Cowan,  Damien de Vienne, Thibaut Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
-Maintainer:  Ben Bolker <bolker at ufl.edu>
-Description: Provides a base S4 class for comparative methods, incorporating one or more trees and trait data
-License: GPL (>= 2)
-Collate: 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 prune.R treePlot.R treestruc.R treewalk.R readNexus.R tbind.R zzz.R
-URL: http://phylobase.R-forge.R-project.org

Copied: tags/phylobase-0.5/DESCRIPTION (from rev 699, pkg/DESCRIPTION)
===================================================================
--- tags/phylobase-0.5/DESCRIPTION	                        (rev 0)
+++ tags/phylobase-0.5/DESCRIPTION	2009-10-31 01:46:01 UTC (rev 701)
@@ -0,0 +1,13 @@
+Package: phylobase
+Type: Package
+Title: Base package for phylogenetic structures and comparative data
+Version: 0.5
+Date: 2009-10-30
+Depends: methods, grid, ape(>= 2.1)
+Suggests: ade4, MASS
+Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler, Peter Cowan,  Damien de Vienne, Thibaut Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
+Maintainer:  Ben Bolker <bolker at ufl.edu>
+Description: Provides a base S4 class for comparative methods, incorporating one or more trees and trait data
+License: GPL (>= 2)
+Collate: 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 prune.R treePlot.R treestruc.R treewalk.R readNexus.R tbind.R zzz.R
+URL: http://phylobase.R-forge.R-project.org

Copied: tags/phylobase-0.5/NEWS (from rev 700, pkg/NEWS)
===================================================================
--- tags/phylobase-0.5/NEWS	                        (rev 0)
+++ tags/phylobase-0.5/NEWS	2009-10-31 01:46:01 UTC (rev 701)
@@ -0,0 +1,147 @@
+        *************************************************
+        *                                               *
+        *               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-0.5/inst/doc/developer.pdf
===================================================================
--- pkg/inst/doc/developer.pdf	2009-10-27 14:44:21 UTC (rev 697)
+++ tags/phylobase-0.5/inst/doc/developer.pdf	2009-10-31 01:46:01 UTC (rev 701)
@@ -1,3352 +0,0 @@
-%PDF-1.4
-%ÐÔÅØ
-4 0 obj
-<< /S /GoTo /D (section.1) >>
-endobj
-7 0 obj
-(Introduction)
-endobj
-8 0 obj
-<< /S /GoTo /D (section.2) >>
-endobj
-11 0 obj
-(R-Forge)
-endobj
-12 0 obj
-<< /S /GoTo /D (section.3) >>
-endobj
-15 0 obj
-(Building phylobase)
-endobj
-16 0 obj
-<< /S /GoTo /D (section.4) >>
-endobj
-19 0 obj
-(Coding standards)
-endobj
-20 0 obj
-<< /S /GoTo /D (section.5) >>
-endobj
-23 0 obj
-(Unit testing with RUnit)
-endobj
-24 0 obj
-<< /S /GoTo /D (section.6) >>
-endobj
-27 0 obj
-(Non-exported functions)
-endobj
-28 0 obj
-<< /S /GoTo /D (section*.2) >>
-endobj
-31 0 obj
-(.chnumsort)
-endobj
-32 0 obj
-<< /S /GoTo /D (section*.2) >>
-endobj
-34 0 obj
-(.createEdge)
-endobj
-35 0 obj
-<< /S /GoTo /D (section*.2) >>
-endobj
-37 0 obj
-(.createLabels)
-endobj
-38 0 obj
-<< /S /GoTo /D (section*.2) >>
-endobj
-40 0 obj
-(.genlab)
-endobj
-41 0 obj
-<< /S /GoTo /D (section*.2) >>
-endobj
-43 0 obj
-(.phylo4Data)
-endobj
-44 0 obj
-<< /S /GoTo /D (section*.2) >>
-endobj
-46 0 obj
-(.phylo4ToDataFrame)
-endobj
-47 0 obj
-<< /S /GoTo /D (section*.2) >>
-endobj
-49 0 obj
-(.bubLegendGrob)
-endobj
-50 0 obj
-<< /S /GoTo /D (section*.2) >>
-endobj
-52 0 obj
-(drawDetails.bubLegend)
-endobj
-53 0 obj
-<< /S /GoTo /D (section*.2) >>
-endobj
-55 0 obj
-(orderIndex)
-endobj
-56 0 obj
-<< /S /GoTo /D (section.7) >>
-endobj
-59 0 obj
-(The Nexus Class Library and Rcpp)
-endobj
-60 0 obj
-<< /S /GoTo /D (section.8) >>
-endobj
-63 0 obj
-(S4 classes and methods)
-endobj
-64 0 obj
-<< /S /GoTo /D (section.9) >>
-endobj
-67 0 obj
-(Grid graphics)
-endobj
-68 0 obj
-<< /S /GoTo /D (section.10) >>
-endobj
-71 0 obj
-(Converting between tree formats and ``round-trip'' issues)
-endobj
-72 0 obj
-<< /S /GoTo /D (appendix.A) >>
-endobj
-75 0 obj
-(Subversion)
-endobj
-76 0 obj
-<< /S /GoTo /D (subsection.A.1) >>
-endobj
-79 0 obj
-(Organization of the phylobase repository)
-endobj
-80 0 obj
-<< /S /GoTo /D (subsection.A.2) >>
-endobj
-83 0 obj
-(Using subversion for the first time)
-endobj
-84 0 obj
-<< /S /GoTo /D (subsection.A.3) >>
-endobj
-87 0 obj
-(Subversion patches)
-endobj
-88 0 obj
-<< /S /GoTo /D (subsection.A.4) >>
-endobj
-91 0 obj
-(Branching and merging with svn)
-endobj
-92 0 obj
-<< /S /GoTo /D [93 0 R  /Fit ] >>
-endobj
-119 0 obj <<
-/Length 1156      
-/Filter /FlateDecode
->>
-stream
-xÚíYËrÛ6Ýû+8]dÈ™Á‹ ¸ô#ö¤õ¤[Y9]P&$q"‘²~}/J–D;åG=Š7 ‚÷ÜàW888ÙÃ÷Ôƒ½Ç$	ˆD”$<Œ’&Hª4£CS\„Gú*¢"ÔÓªŽb÷`š(f˜†ãy‘kÿh«èïÁï`N¬™ãšZk¨ž|ŸVìÑ]_‚Ò$¡®oLE\&ALR)õŸüQj«
-À ôaå~_»"+ßû¶]vÕô[Û½ëüÎU2¬ìdÑ’»‘ÈÅHd7xQnéßR¢\!`õ“ô¹@\1 Ïç‰ÿä\×VÏæ°ôx„¼÷ähDBŒSo‘*ðb\t#AÌ)ˆ‘z‹‡U1Zí«Æ}	Šbp)‡Ì|zM€Ø EŠRA…³*ð‡a´†I§4	?]ÓTŽ_˜Ï/mˆÄO›€c0Ì›Î-ô`,ÝÇ[-L´Øgñq”‚f¬Ÿ‘yăy1Í‹rìýÏðŠ{üNí—Ä6<Ê8G’=†%_gÉ=ËÃNG4fŠ…ÍÊ<3y³î¦XŠ,UCÆ됉‡üRÖcYÝØ"ŠI¸ ¿.ìÄ?¹©ÒöÜ A%æ
-|¼=
-ái|®ÊXßÔíð+cuîG󲝗M˜1ö àÇjEAX~)üÂöTÐeDU8)]9Ÿ5 at cgˆ¢8ÁøÞŠ§ÿÙeªsÃgn…ZÄ¥Ÿ)ëòYý1ßÜ4.b!Õ3
-f‡Äzf]N3ùÄÜÞbU„üÓñÕW}]èÓè2ÖåDéEŽä—Û’žK¨'Z@õÄ…8wð£Ìf›8œ‘·øòâÚˆž6ƒ$•Sè8R<4Ù¬‡8§;9ó_Áf6œO5ìhù‰©z{šTô-Ô¿@¨ÏMæVÃõ‘¶Y1mnEé”™ØåHð¢á¡2¹6ŸÊ\ßô 0¥¿œ›ŸdKâ[貑ˆWÈÕÛ¬ô·ÙÁDûûëg}3w™'ˆ‡Ó¬i|ëi14™ùîdí•;"aîû]Öuï¶K˜”KÒÛ\³•'vÎ=è¥#£;fYÙݶgÚNºÄ¡z
-'¦èàÆ&«'Åe?·A™Øj‘‐`ŸC£á•+´±]Z…»ª´u™µëö¥ŽœíKkt§Þ¨2³Ìnzé+aÜTó2­)êß|cÑ4sÝô(“äQNۏb$ÏçՁ4÷dê–I¬dë¼HÌR‚°\߁ö‰b)iø§geñOÖ¦
-c—©F®§Mô©5V(½/¯ºŠ›`ÄÒ%£ëö.Y5…­`¡l^÷Áá¯rߺ+$Û„€˜‚ë‡Ñ}D½_?•Áñ
-ÌðÔ•+º™Ñ
-s÷V™¶å+LÓXÿÃýÓkÊånd›’'ˆºûˆy_Ÿ/,×\gÖçûË^`ö–Å€(+žDîu80Y龜û~Kf.p™q׺L[»µqUöo
-ÉN¹Xn¸¸{K”BœÁ6.TûçF÷ÇÏjߏƒ½±áÃÃ
-endstream
-endobj
-93 0 obj <<
-/Type /Page
-/Contents 119 0 R
-/Resources 118 0 R
-/MediaBox [0 0 612 792]
-/Parent 130 0 R
-/Annots [ 94 0 R 95 0 R 96 0 R 97 0 R 98 0 R 99 0 R 100 0 R 101 0 R 102 0 R 103 0 R 104 0 R 105 0 R 106 0 R 107 0 R 108 0 R 109 0 R 110 0 R 111 0 R 112 0 R 113 0 R 114 0 R 115 0 R 116 0 R 117 0 R ]
->> endobj
-94 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [99.35 522.744 179.452 531.655]
-/A << /S /GoTo /D (section.1) >>
->> endobj
-95 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [99.35 498.889 156.379 509.655]
-/A << /S /GoTo /D (section.2) >>
->> endobj
-96 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [99.35 476.695 209.7 487.82]
-/A << /S /GoTo /D (section.3) >>
->> endobj
-97 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [99.35 455.054 204.514 465.902]
-/A << /S /GoTo /D (section.4) >>
->> endobj
-98 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [99.35 433.136 237.887 443.984]
-/A << /S /GoTo /D (section.5) >>
->> endobj
-99 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [99.35 411.218 235.057 422.066]
-/A << /S /GoTo /D (section.6) >>
->> endobj
-100 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [114.294 401.2 164.523 410.111]
-/A << /S /GoTo /D (section*.2) >>
->> endobj
-101 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [114.294 387.308 166.819 398.156]
-/A << /S /GoTo /D (section*.2) >>
->> endobj
-102 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [114.294 377.29 173.24 386.201]
-/A << /S /GoTo /D (section*.2) >>
->> endobj
-103 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [114.294 363.397 147.282 374.246]
-/A << /S /GoTo /D (section*.2) >>
->> endobj
-104 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [114.294 351.442 169.283 362.29]
-/A << /S /GoTo /D (section*.2) >>
->> endobj
-105 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [114.294 339.487 207.916 350.335]
-/A << /S /GoTo /D (section*.2) >>
->> endobj
-106 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [114.294 327.532 189.028 338.38]
-/A << /S /GoTo /D (section*.2) >>
->> endobj
-107 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [114.294 315.577 218.487 326.425]
-/A << /S /GoTo /D (section*.2) >>
->> endobj
-108 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [114.294 305.559 163.388 314.47]
-/A << /S /GoTo /D (section*.2) >>
->> endobj
-109 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [99.35 281.704 294.386 292.552]
-/A << /S /GoTo /D (section.7) >>
->> endobj
-110 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [99.35 261.723 233.339 270.634]
-/A << /S /GoTo /D (section.8) >>
->> endobj
-111 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [99.35 237.868 184.919 248.716]
-/A << /S /GoTo /D (section.9) >>
->> endobj
-112 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [99.35 215.95 404.038 226.798]
-/A << /S /GoTo /D (section.10) >>
->> endobj
-113 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [99.35 195.97 170.556 204.881]
-/A << /S /GoTo /D (appendix.A) >>
->> endobj
-114 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [114.294 181.801 321.738 192.925]
-/A << /S /GoTo /D (subsection.A.1) >>
->> endobj
-115 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [114.294 170.122 288.115 180.97]
-/A << /S /GoTo /D (subsection.A.2) >>
->> endobj
-116 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [114.294 158.167 221.808 169.015]
-/A << /S /GoTo /D (subsection.A.3) >>
->> endobj
-117 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [114.294 146.212 281.971 157.06]
-/A << /S /GoTo /D (subsection.A.4) >>
->> endobj
-120 0 obj <<
-/D [93 0 R /XYZ 99.346 730.572 null]
->> endobj
-121 0 obj <<
-/D [93 0 R /XYZ 100.346 692.71 null]
->> endobj
-126 0 obj <<
-/D [93 0 R /XYZ 100.346 535.793 null]
->> endobj
-118 0 obj <<
-/Font << /F15 122 0 R /F16 123 0 R /F17 124 0 R /F28 125 0 R /F29 127 0 R /F30 128 0 R /F8 129 0 R >>
-/ProcSet [ /PDF /Text ]
->> endobj
-158 0 obj <<
-/Length 2866      
-/Filter /FlateDecode
->>
-stream
-xÚµYmoÛÈþî_!äCCÖšË]¾½’àR¤—4hbà$AJ“”Äš"uK2¶þøÎì)RfÛ¹û"îûÎÎë3#w±Y¸‹œ¸ü}~~röÒ‹R¥oq¾^H×Åö"ˆ<êpqž->:r¹’ÒóWÕRI§5õr߬KÛ¢®–ŸÏÿyö2ZÄ"¼ Ïp+OŠÈ“´û|[4Ë•ÖžóµØTyÛæØSN?ZTK/rÚ¼ÊòŒF’†V$ÔÝtE–Ss]šj·<’å_q{^Öû]'…NKõš(Sîˆ4/TBAÓ%ÒöÛ›²¾Hšüö#|O(Wõ“ª'®7ù~¹‚»ê¦hksCƒtãb¥<_^¼ ¦‰Ø÷é„6O‘ÎmU¤I‰üSNU·yƒMK¬Ú›b—ày8Ø3ÆäMKÓmÍ3íÓ†FFÏ‚ aøDK1®¨ÛíR:À-éôsãƒs^cvnSÓõxt›%où}.Á7ö™îô}iM‡šÄ«4‰H)KAnf„IúÅA‰ðlT"¼lW›þ¶5}“Šfø±¨´ðÍ:`FŠÌ°ºkWþ…>]“›§ýq‰ÝÕ%¥ z¦V²’J×W(kƒ¹XÊ<6“w«—ËX;µÙäß5Ž·ÁYÃƒGNKEµFž°¶®ã¶fÁ)+’ȹ¡q¼9RöæS¼,ÝQ?±†xÄåâÖЯàÂE âPEÖF<x[,JÒï Fncú P„‘FV“êYÒӲˬŽ+kÍ8ø¾³JDjk–‚Ç&L
-?¹¾Û ´òüï+à1(×DEŸíÙFª¬¸“
-çÙäa‹0è;rÕǹMu>ÓeÃÄý¶´ì“MN»ýãS7’¦È+B£©;“òú”ž» ÑpT¯Z§0Çh­Ö+]ZÕC÷€wÇ]tj²1m3güƒ³Yç	k©D'ù{¦y¼*Æ®ð•k¢w§&Z¯{K”x²¢ÚP§,€(¦Ÿ:ö£¨kèK¥³³j7X"®)š´kXc¥:œ>°q¸"E†¢ßMª=³{Y
-_6VÄ‘šr³—"Í Eñh&úè¢&æ¬î`âJ…"ŽC È~8„pÔ¢(<8xچǬ¯t¬Ù-jÌ®g©dwªï 2J²¨y5¸™Ôdà
-Q¶­Q*WÔÁØ©£`ìhi ¡ù}o
-¾ï$ýÛº$Oå#¶ya¨yì•qì-Ç)CáGÎgŸ˜¶H»2¼ vŠÝ`RI…Ò¶ƒ
-}mèÄF“Ʋ‰ÛVÛìªfKK«Ã7ý)5}¯ð½µ¹äÅuGÒRëwÕuRŒ›^è‚æív¯ 肺<kþ–¨A«1KÝ+ÎôDõèÅà¿(:“qAs>‚(,fî—®n4`¾æëde äñô¬‚e)¥7}ï[{a4òv*d܍c0MD‰(þE#=HÏpp&ø…,!»µ,I•ù¨½ìVæÈEÛ±‚WÌ¢_¥cÞý®T E΋™ŒXÕ´@Á¦¬0 °%£‘µ©wsò@Ï"½žŠw3Š ¼î1þRÞ˜:鹐xJÅ2¢•_®|@_L >_ÔŠ'ÃSŸœÒ*`xÝPó'ú<Ù¶íþ¯ggfµFÙ	³Ú›ú¿ðÝ'6ØÎ Aw
-CÀç]Qf¨°vø¨Ñ–(:’÷¯œ ÆW6S-v«„žëKô˜À}Ìa'†€>&k*
-ZªûÂñÁL­íá¶N‘oJÞUaZUÞ“DِÜ$»œ‡ÈâkÊ9b‹@¡2¶DˆàYgT2péasá5ºCÕ"xtØÏm“—kú 1æò¤ˆÅÐÈj›ù¥]ŸnÚÁ„e2|û|Kn´C¯0ˆØÓ¬­@ äì®xÿ³lWT MÌhò(yTdU:ÚóÆ À¿3´ñϿ⸦]_HWN%p´ï1“ aºª"íKç
-x<;úö=}?Ї·>µÊ}VhY±ÂÎmrpô<³åFÖ'µÇù/í<èÒãçÅZD ÎF¬îdœö'|³aHý­¨²ƒûþÖétà‚ŸjÎïʱ«•}v-O‹ò
-!ˆñóóöÉ£ µ:žàïðîL08ÂßLÎœeýkŽ’мåA4ÛÀJkM.&ª‡»
-/?¨t^Söß]Ÿ²è
-x;8Vá0€Ð
-nï†0è%¥É“Œ;—U'±wEÑZ“ý(Kô ¡rΗ‘FІÃä l“¾’Ñð]/xMnjbÃðÄLO¸Zq6{Û™î ÎYÛgC¼ ãRkÿe4>þ@d¤=ìâ ÿIúBHWù æè[N Â>{{h±Ac-¨¾…¸  ˜F)rQéÏSé¨T6kA©ºC!§,.—dnç‘X~ýx $ÃcGyFôRÈ4+¡ü’ˆ¡†õðýpÚ¿Þ’¸z]|ÑÎûôX©ºeH8uyKß¿Òi+à½rbðñï¢©Ë#ºµû<´Z°†·6ËÁ¹ƒ¶@]|tpñ}i`Š#§®½)@Ѓ6Y%ÓÈ´&„ëW«íAÖ÷èQ®A©ã£ŠíoÈKS´óxIÂ÷ïF¾? ¼_®Û¼๚æ̏P‘±šDvéÉëVáÒï àC^#ûL›Pë.ì“û}Ø[e‰ÉšïÖ1-³,èDd˜ btMƒã[^Ùçxt!Ì.´ó6§‚áç{¤ºÂjóA]k€‘SžÝUÞ”
-Î&Jþ/@¬ àÁ§ìÈm.g
-ˆÖ™ÅŒê¢QÞ_”7l»~$\÷È…®»ŠTG8„>´ÿ‰D—/¤­R74Ôlë®äé!'ÃNQÍüHB< üñbàëP¸á(ƒ<Ð)_Š"±ôп:кb±Ö7Ô«êj5<Å´=dc°ãyàà Ïò¡!KMƒihCÖûÉ•úšì.. jCK:ÿO±PDœ£Œ 4¬»­Íg$µ–ŽîEÞÂò’¯:¤¼p[¬‘Pw-[–|û¯‘C‘‚*\¼
-‚ Òƒlhi‡éBû ]èhž‡×º\Ö6l“‹æ;Û“_Õ˜-f,éXbB´d=¬-±Z„7tM>›^Aª^ðo«™ÊŠ†dÈ°Ö¿[ûåüä÷ô’îBÿ=z^°S.ÒÝÉÇÏî"ƒIà©PpÑ•]º[H,OÄXT*ïOþMÿdÊ°B†\e ì
-&ïrŠt<þn²Ç\.ú:	%!žÅ!ä7IIË6%¶[¹:€y1ðʦƬ€e6XoPKû~_7Àufsä[&D®øžÀVŸFî!ÑRaÿ*Ý0Iž3*eœaµú2G[8ûycênÿ¥È~’·œà7	õÆEä?“P,ÚŸýŒå×GP)ÇEä?“Êw4ô翼I*ÌSöÙútú?Lgj¬2+a‚Þœeu
-üDâšžâë
-bÛîÊJ>øaZ³ü+* $í¹É~_æ"­wgmžn«ºD’77g×iå¢OŽsÔ¡ïêê
-­w×àÛ–ÚtTØ1%x[K(zö@îE Î›£®í6l&i›_?”ŒøcRq	×[Jî$’WOäÄXõ4ðÞ?@éóë¶ù¾Nhõ&ña´‰­¸Ä€+ÖÛÔ¤–_ø¢Føûå=Jt„¶ÚŽ¿Gá5¥B0$ÈÊ›û“bìÿ§Qè
-endstream
-endobj
-157 0 obj <<
-/Type /Page
-/Contents 158 0 R
-/Resources 156 0 R
-/MediaBox [0 0 612 792]
-/Parent 130 0 R
-/Annots [ 131 0 R 133 0 R 134 0 R 135 0 R 136 0 R 138 0 R 140 0 R 142 0 R 144 0 R 146 0 R 148 0 R 150 0 R 152 0 R 154 0 R 132 0 R 137 0 R 139 0 R 141 0 R 143 0 R 145 0 R 147 0 R 149 0 R 151 0 R 153 0 R 155 0 R ]
->> endobj
-131 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [323.441 578.762 329.903 591.355]
-/A << /S /GoTo /D (Hfootnote.1) >>
->> endobj
-133 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [99.35 566.807 155.798 578.762]
-/A << /S /GoTo /D (appendix.A) >>
->> endobj
-134 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [161.214 566.807 210.059 578.762]
-/A << /S /GoTo /D (appendix.A) >>
->> endobj
-135 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [230.633 566.807 262.173 578.762]
-/A << /S /GoTo /D (appendix.A) >>
->> endobj
-136 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [189.884 555.405 196.346 567.445]
-/A << /S /GoTo /D (Hfootnote.2) >>
->> endobj
-138 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [152.291 545.387 158.753 555.49]
-/A << /S /GoTo /D (Hfootnote.3) >>
->> endobj
-140 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [207.596 531.495 214.058 543.534]
-/A << /S /GoTo /D (Hfootnote.4) >>
->> endobj
-142 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [494.757 396.972 501.219 407.074]
-/A << /S /GoTo /D (Hfootnote.5) >>
->> endobj
-144 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [394.213 383.079 400.675 395.119]
-/A << /S /GoTo /D (Hfootnote.6) >>
->> endobj
-146 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [240.844 371.124 247.306 383.164]
-/A << /S /GoTo /D (Hfootnote.7) >>
->> endobj
-148 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [339.681 347.006 346.143 359.253]
-/A << /S /GoTo /D (Hfootnote.8) >>
->> endobj
-150 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [137.264 335.259 143.726 347.298]
-/A << /S /GoTo /D (Hfootnote.9) >>
->> endobj
-152 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [229.391 323.304 239.824 335.343]
-/A << /S /GoTo /D (Hfootnote.10) >>
->> endobj
-154 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [343.462 268.537 353.895 280.576]
-/A << /S /GoTo /D (Hfootnote.11) >>
->> endobj
-132 0 obj <<
-/Type /Annot
-/Border[0 0 0]/H/I/C[0 1 1]
-/Rect [114.593 214.201 278.481 225.697]
-/Subtype/Link/A<</Type/Action/S/URI/URI(http://phylobase.r-forge.r-project.org)>>
->> endobj
-137 0 obj <<
-/Type /Annot
-/Border[0 0 0]/H/I/C[0 1 1]
-/Rect [114.593 204.696 329.291 216.193]
-/Subtype/Link/A<</Type/Action/S/URI/URI(http://r-forge.r-project.org/tracker/?group_id=111)>>
->> endobj
-139 0 obj <<
-/Type /Annot
-/Border[0 0 0]/H/I/C[0 1 1]
-/Rect [114.593 195.192 316.589 206.689]
-/Subtype/Link/A<</Type/Action/S/URI/URI(http://r-forge.r-project.org/mail/?group_id=111)>>
->> endobj
-141 0 obj <<
-/Type /Annot
-/Border[0 0 0]/H/I/C[0 1 1]
-/Rect [114.593 185.687 317.087 197.184]
-/Subtype/Link/A<</Type/Action/S/URI/URI(http://r-forge.r-project.org/R-Forge_Manual.pdf)>>
->> endobj
-143 0 obj <<
-/Type /Annot
-/Border[0 0 0]/H/I/C[0 1 1]
-/Rect [114.593 176.183 329.291 187.68]
-/Subtype/Link/A<</Type/Action/S/URI/URI(http://cran.r-project.org/doc/manuals/R-admin.html)>>
->> endobj
-145 0 obj <<
-/Type /Annot
-/Border[0 0 0]/H/I/C[0 1 1]
-/Rect [114.593 166.679 319.827 178.176]
-/Subtype/Link/A<</Type/Action/S/URI/URI(http://developer.apple.com/technology/xcode.html)>>
->> endobj
-147 0 obj <<
-/Type /Annot
-/Border[0 0 0]/H/I/C[0 1 1]
-/Rect [114.593 157.174 290.685 168.671]
-/Subtype/Link/A<</Type/Action/S/URI/URI(http://www.murdoch-sutherland.com/Rtools/)>>
->> endobj
-149 0 obj <<
-/Type /Annot
-/Border[0 0 0]/H/I/C[0 1 1]
-/Rect [114.593 147.67 226.675 159.167]
-/Subtype/Link/A<</Type/Action/S/URI/URI(http://www.tug.org/mactex/)>>
->> endobj
-151 0 obj <<
-/Type /Annot
-/Border[0 0 0]/H/I/C[0 1 1]
-/Rect [114.593 138.166 209.738 149.663]
-/Subtype/Link/A<</Type/Action/S/URI/URI(http://www.miktex.org/)>>
->> endobj
-153 0 obj <<
-/Type /Annot
-/Border[0 0 0]/H/I/C[0 1 1]
-/Rect [114.593 128.661 325.057 140.158]
-/Subtype/Link/A<</Type/Action/S/URI/URI(http://cran.r-project.org/doc/manuals/R-exts.html)>>
->> endobj
-155 0 obj <<
-/Type /Annot
-/Border[0 0 0]/H/I/C[0 1 1]
-/Rect [114.593 119.157 298.656 130.654]
-/Subtype/Link/A<</Type/Action/S/URI/URI(http://wiki.fhcrc.org/bioc/Coding_Standards)>>
->> endobj
-159 0 obj <<
-/D [157 0 R /XYZ 99.346 730.572 null]
->> endobj
-5 0 obj <<
-/D [157 0 R /XYZ 100.346 692.71 null]
->> endobj
-9 0 obj <<
-/D [157 0 R /XYZ 100.346 619.789 null]
->> endobj
-13 0 obj <<
-/D [157 0 R /XYZ 100.346 447.463 null]
->> endobj
-17 0 obj <<
-/D [157 0 R /XYZ 100.346 309.287 null]
->> endobj
-163 0 obj <<
-/D [157 0 R /XYZ 115.59 227.501 null]
->> endobj
-165 0 obj <<
-/D [157 0 R /XYZ 115.59 217.996 null]
->> endobj
-166 0 obj <<
-/D [157 0 R /XYZ 115.59 208.492 null]
->> endobj
-167 0 obj <<
-/D [157 0 R /XYZ 115.59 198.988 null]
->> endobj
-168 0 obj <<
-/D [157 0 R /XYZ 115.59 189.483 null]
->> endobj
-169 0 obj <<
-/D [157 0 R /XYZ 115.59 179.979 null]
->> endobj
-170 0 obj <<
-/D [157 0 R /XYZ 115.59 170.474 null]
->> endobj
-171 0 obj <<
-/D [157 0 R /XYZ 115.59 160.97 null]
->> endobj
-172 0 obj <<
-/D [157 0 R /XYZ 115.59 151.466 null]
->> endobj
-173 0 obj <<
-/D [157 0 R /XYZ 115.59 141.961 null]
->> endobj
-174 0 obj <<
-/D [157 0 R /XYZ 115.59 132.457 null]
->> endobj
-156 0 obj <<
-/Font << /F28 125 0 R /F8 129 0 R /F30 128 0 R /F7 160 0 R /F32 161 0 R /F16 123 0 R /F19 162 0 R /F31 164 0 R >>
-/ProcSet [ /PDF /Text ]
->> endobj
-179 0 obj <<
-/Length 2972      
-/Filter /FlateDecode
->>
-stream
-xÚ•YY#·~ß_!øe%`‡ÓdßA^’Ø»Øda öyX0GÍ‘:Óê–û˜ÙMþ|êbRÏÄ~Q“Å"Y,Öñl›`óáM ß¿Þ½¹}Ÿmr•'&ÙÜ=lt¨0J6IfT¥›»bóyk»®<Ô'WïL¶íßínÂLom]@#ÕÛse÷Ž›Ýš¶ÍÖ>ô®eò¾9l'óÊš‰e]¸/Ì<[ìa¨÷}ÙÏÞV•püÄ좷ê v¿Üýýö}Ìäã@éXáHââ᳁ýboÍ/Ì>?e«8™qóëoÂ<VIn67Z«<Ž™·s¿¡$Ú/._ØÈúz§4TÆÄ~'TAnë¦_ÙЄ*[È¿&yÍ0ôlM»²Ž6Ê‘g6ï@ÈëãTÅáÈ­¦S˜l£#´CÚ0AÚH at -Få` ÄÃ…h8þOuÙã5ÅÛÞu}Y¸ó\öGný°5s]	ÀÚZeFó’ÿÚeá.Úä`­4ÐfðÛ…pnhd[°¶Ž)ÍOÍΤÛ'’èC+s½d¼àCk»¾öýà7é›i“•ÛÉ´2:õŠúÁ\)PY?9hQÖ7W¤€—¥›Dåi˜Ñb	«Ù„*Ñ¢Imd1ö˧ÔpT?ñƒø'÷ŒþØ´jw~¿`ßÔ7¸ÌЙJõÒ„û¶¼ÐÇгt ¾ûáÀŸ±kB§C§;îP“1êí=l“â%aÇîÁ½Ï¶._¥úÊí
-Z¨~YñùXîñ’ŽÓˆ´ŽN–°°PÓ[ÁJ´0,X‰.?‹Å>²4@æQ8¦ÛŽ¿Ï¸­«ª%•ÂJ'<øÙ¶s26…çáç£íyôhÏgÚÈÕ~‡£«™Kd‰g!
-{eÇÃgª¨1D¦¸ÓYÎHd°O4صóR`
-¶µ;ؾ|ÚÉm ç'ü½gÉ$ÿ—ÇÝÓŽÄe"K‹ôþØtÎæó ‡í%ðMý¶g¦“}¤ÙìáÐŽÆM'c˜î:FZ×7-Y´}
-X÷4V±ô²îú[´£;\õö:€€c†é9ËÖía/Ôa²qSƒÝ<ÚÖà8ž¦ÛB	 ‘2ᶃ౗6úDåFYæ·®chüV}#ù£sì†"âÒ
-iH”e½¯†‚d‚žè›,;ÒVõ¤5$Œð:"-µc2•%S^”°9ødnÅ2a—´*j-ì(Âõ¶¬ºµœ«!ç†Áàhýád/ŠYØ/žv`DVÄ:€rÃä$öLOb‹zÛrZåð†Å'š£øÕ—`Ñ”–Âh;;æ“\9`{‡£iý°’=•	/“;,^}åF‰Ü{:WnÚŒ†é6Òí%D—;ac~1²ä /×ÃQÞ­¦f¤*H²ejN$5¹À}9c0…ãöì‚SPêþoB¾;ºŽ,5˜Mº1I..…t¶rl”ݵ®™gðs_Pp‰2ñ<¿V
-Ä~·‚Ør•Ž|ˆŸhQ:h†Ng¢í;a{ÙöÔtÂ;J˳A¶+gpÛœí&ñ…͹ªs/[÷n´6¹eŽq at Z[80}Š¥JC]¤ûË7ëL@ÙþX§ù
-F 9Ãkè/xß1¥§Ô¨GÚ	u‚
-„ýè!„»5æQÛË
-8ÆfêZÆö0Ä0Ë\˜ñË«“Eþ®¤$áxðóñl05«sÔlíÿ:nJj÷ÒL~-Å‚{»GÊ£8cÃT‚ZKoÿ6à•´¢¼3ö]"µo
-¿GÈEeá¦]×`"8æÎíP¯X³ÉU”ŽL'Ù—ñÊ«fÛšBÐMì­£u¶wß·˜ì¿”O¯ù?Ù{°èW*…`2¹ÜO¤ƒ84¡¿r§/OŽ[••ËÅ‚øZ©ƒì†…U˜ì(åâl
-œDۏƒ½¸ÍêòO¥]+Ú¢Ba¾D‘‚•?߬„ñXE:ŸUU`‡˜Ük.¸ Ñ˜´®·LÖgá"„E+u[¤¢|L•
-’Ý¿ÁV	*¤Û=ïÙÄê¸kù³ô·PüÍP®Nö¶.ñ¬Ö†y ‚lÌhßÿôéÓŠuF*˜pEù ¾ &0ÑÒkJßY´¼¯ÇSZ%WF™ùàjׂ
-¢Q žòiã@‘Pr]”{1œ!`:š‚I꫐–gp	 œå¹ãÃ'Zl‘•p_pF½„׈Q"P!a*°ç©?Å:‘èÉ%FT)=P|n£ïœ}ý„$`
-¦¬ÁiÅpÔ³ÿ¬ÃÎk~ÃK2+âiS9í7ïкB
-´+çtå(•gŽq>x.µ†”Å#ÁVÇT~J`«jTð7L[?£bþšs
-ÜÀë!l1ˆ¹Œ` ”ååØiçÑ,š0èY_¹9+ÉÂ\²¶öVH“α·4nœO€PÿA–À°vµþN&ŒdŒÈ ö©ø¶îŽîBr4¨$K—!lLÊ©Õ¤ˆ<#ÖÀ÷5,"-³üŠ8ê-³qZöã\UHÕ™.¼ÏfΗúª:Ö‹Kä çK/£ àüPqZ»´>>~”Aö톪ç6•Çðµü™>ìÓFð•Ò˜ÚüÊ4›´.&`
-8Û‚k­(Íü5xË…,->@±—|áŽ{á½n)HG{hš@+¥àË/9K{€žOö¨|@¶/•‚ÍüÙ {LM<1¯à;™*ö|F ÖR¦¾ T‚XéÈŒ2]¢‚0 ¡ÐÑåR4+O+s*c<i0º†Œ¦éòÜ'ûÈY–j¶“TÔ­m¿NUU'UÓÐN¬ë•q*æ¿„™?ÂŒNU¬³‹Äyÿ[ÛÛ×AX²à¿kpÆ{¬Gv»î?£ÖҶy- ¦™2ÁÞبbÂÍaÊ’ËC‚··«ïÉZééåC[+ÊwHFÌphíùXîiÑdŽvxôCËc8‡<!a=‚Æ‚EkÑ}ŸA°à
-â3A âè—p%9ÜßCÍíßŠUXÔ£T¤XˆÍDÉ÷øÒDY Êv¨° ìG&-=3Ka…*+‘CbŽ«™nï+Ç”Ð3.õë°N±q±†¸×37!›¡“žGMä7"í✅Ãw©š Fœo›¡ç%Š9V"ñ	ŒÒœ+l5~…×2AWÚgÊQ~[jÈU
-a6
-t’óiC¸¨ž˜± Ë*À×I®b®\wT¬þ]%Ñ
-ì–\(±Ð3Y:RÇ×äno+~«Å+ÇW*–džΏ0( ’e‹5X·òö[5=AßDn¸¡<#ŒbiZ'×.GXÀ)-vOþY™ž#è)t|‹j^
-™QªÒxôð¿çoååoŒ9×êÅ'Hg׆ñj Íb•éL÷â†/þ%Á"ù2ÂEa0ËMØóÔõCçF¥y¶ræÐóífÉBv%›}q#HŸñè>¯è3Ö*ŒgQ”c<Ø 8`&—¾ßíÛRB €€Äž¦WpÒ4l­ àµù½H³®ÍÀ
-jhúËÖK#6`Ç!~, 1™€ULEa:¼@6‡Lö¨A'F%ÁE˜äXþ‡_þ¢|û‘žUðZ‚þ‘Ã-úk‚(Õ~¨8á¡W\Ô4±ü
-\YhŒa ±HK¼•¬/¼¼¨£¼s=±Îíù»»7¿½Áwñ`£Ç¿ÝµÉT
-½?½ùüK°)`p³
-ÁJŸ‰õDo¦IŽÖTm~|óOþL3VyšÊ­‚/g¸˜QÀÎùŒ°­ó¸ñ-üo2Ô@¨i ÉXU†z6`ð¡<Ú÷ýùO··û–jMÕÞìn’ÿƒ¥ŒÐ·Ïîþöl÷øtKÿÜr-쾨cªVÎΝe€ßR„È
- *É^*ï’¹k„
-endstream
-endobj
-178 0 obj <<
-/Type /Page
-/Contents 179 0 R
-/Resources 177 0 R
-/MediaBox [0 0 612 792]
-/Parent 130 0 R
-/Annots [ 175 0 R 176 0 R ]
->> endobj
-175 0 obj <<
-/Type /Annot
-/Subtype /Link
-/Border[0 0 0]/H/I/C[1 0 0]
-/Rect [406.718 613.092 417.152 625.131]
-/A << /S /GoTo /D (Hfootnote.12) >>
->> endobj
-176 0 obj <<
-/Type /Annot
-/Border[0 0 0]/H/I/C[0 1 1]
-/Rect [114.593 115.446 349.964 126.943]
-/Subtype/Link/A<</Type/Action/S/URI/URI(http://cran.r-project.org/web/packages/RUnit/index.html)>>
->> endobj
-180 0 obj <<
-/D [178 0 R /XYZ 99.346 730.572 null]
->> endobj
-21 0 obj <<
-/D [178 0 R /XYZ 100.346 653.288 null]
->> endobj
-25 0 obj <<
-/D [178 0 R /XYZ 100.346 527.344 null]
->> endobj
-29 0 obj <<
-/D [178 0 R /XYZ 100.346 475.635 null]
->> endobj
-181 0 obj <<
-/D [178 0 R /XYZ 115.59 128.746 null]
->> endobj
-177 0 obj <<
-/Font << /F8 129 0 R /F30 128 0 R /F28 125 0 R /F7 160 0 R /F19 162 0 R /F31 164 0 R >>
-/ProcSet [ /PDF /Text ]
->> endobj
-184 0 obj <<
-/Length 2928      
-/Filter /FlateDecode
->>
-stream
-xڝZKsä¸
-¾ï¯pÍ%ê*7G¤¨—sÛ©Ý­Imö0qj;s`«éneÔRGRÛã­üø ¨G›öTrq“ H‚ ð ßnâ›_~ˆù÷ÇûÞÿ\Ü”¢ÌTvsÿp#U*TšÜd…¹Îoî÷7DçãFÑsÓí.»]c‡Í6QyÔ؃m÷b³ÕZE÷ÇšÉþ·µ•Ó?Sw·ÙÂ_[™Ë`‰2í<T„†²è´ÙÊÈÔ-õh{b97ÝÈӁº‘ ÎæËýßàT[)E™¦$zepn¡£j¬GÓ,õÝšE
-õŸL1Qhs ð@ªa}í-ÎÀc§eý8Ií&·I9¼05+O¢ßEGÓCU]úÐIœÀ™ŒöõçX&¶·-^ÊHÄÇÚ>Ýô®!Ɓȴa&gq 
-*i;ž÷µíp•§{ŒJAÅs¯{¸Zíd¼0,<0Uu_‘i ùsœÆÀýL=ӯ玅JPkcÆú…ÁMÐ®ÐP¤3œÎT^8 œò¸IS0“Æ°!¸œŒ´@ÝSs©¦Q€”›¼áýÏI¼ð…­Ò¢ŒshHB©»~oûíÞ~»šºô¢4ªHaÀMaßÈãèáÒVcÝ¡`¹Œ<µ2Mãô ´‡¾;Ï
-;\É$µ¥ö+÷Ö‰C|Kt,’8ñl';ɸœÝ¦YôqäMÌW§òv7‹®,óK úå†I*â|Ú°ëC¢+‘æz½ÐþåJÛ$…Rzm,€Èý/ò00b8€ŽKò-×€	–;öu{ RÝîë
-¬Êõ%iÔ
-ìÁ‡{Ô¸£ö–ÉN—À}]UFà‡ÞÉšgæh-MB—@Âg™è3ßÂ;
-z¯c$ËFbwÃUüÅAK‚VœE¦¹8`PdðkèÇûž½ë™ÅŸÔr EcÕ™0—æÌ΃þ¨Ü{ ßi®Ý¸u2 Ðo¡±¥fxê)¹,ÐÁ»=âA-,žXKF²,Z냗 ŒÁ)R÷ÃH–Z4wÁ7±¨nø	Ѿ»4{æ¶ý©nÍh_V‡$„;õù–OǺa”ñ<þ®™ÕCÓ,,tX"B³0Àqnk:ê;wKG¡‹³y…*ÀÝE¢3µB£€Ñ(‡»…
-ƒ«åiô›ýv¨ù¡17­w=EbèP8‚Ƨê|ö
-Q¹ÈË’-xÑhâ«p!;\ÍfPI "
-«U
-Z¥äU~ékžqèÍùXWChO3û@GXóÿØžœ7ITRF¤?m°Q‹w’–ìÀÈóÐõ`uHPh ëõÝ¥ÝoÁ>ÎïˆX['(Så%D.ÊD‘,ÃÅ!\bV%E¡$±þ¾—sö§£áè
-NOfz'«ê³J@™ ØeG;®º–2õ#
-zWKÁJŽä)zqXšþp!	©¾ÝR€§{.tÕÀZ‰(fì 6d‰\¬!ù€-{àkËJ§¥ŸgÎöîΉØ@AD›$¸
-¬€\ˆ2ÏØ»}¼¾TÇ»;üXS‹bÞÝŽ¥ ãX òθÔñ+õžj°úËH¦œ}ª4~—#S§n\Féëˆéc‡MÄiAë;EÞ‘0D
-"Lî†[ 4#Ñ~«ìS‡ú3´ où$+\›,Me‰Ó¿¤Ó)¸—'0£Pz‘f"IŠïZŒq<é
-ñÛ;L¢—ö—‹,Ÿ’ÀWÉBäj2§7°j—"¡ØãÑ´$±ÃKl°àèäHÇ>mü‰Wàëæ#ü¹%;"pâˆÐ[ïýnõ€:º%¥Ê$ƒh­T2脪ØЍH¡Ù}ÓPbø	7ÚÕ‡K=ÖJÁÀà°zJ9¼¨9 x?O‡D>dñºË8‡óÆ'É”<›	LÜ!I¼z¸evJ
-»ÛPXÜ¡•#¾Öü{2láØ™a:®$ɪK3þ‘ò’½…œö™ v’8—º€vÌb?2Ó=® ÃtèÀD®7èDX!B	bûÆê1À8KèT ¿;¯
-ÔëÊ65'	ëàŽwW¬ï.X\ðE¡M¸ ŽÁ»ÔWöóÑkFCÆâÍUgK‡vC“~±CaB»T‹~±æ¥ÈÔ’píùaƒV㋝µûeJÈ|òw¿úh1—Á–ý÷Å4`  q–ù?ÌâjÏÌMŒ´»zÜl¡ùŽ<I)ô¤+džÖF£‚0ŠFYø¸çSэMºó®±½™Ê^ :¾„©
-¨¾&L1íóËs«XÈ,ŸâÙTRWvÞÑýÒ¥bâ
-	Ìß;çÏ@nØsw	¥{(ÉÚ³ráÚ…;ò·!Aðå*·IÒf’•"—W†åÔr9AV_q­ëjbtˆšu‘ƒ6SÙïß$ª ß0“]“®+˹°Ç*íkû½£êz®4@í~–@¬sê÷éŸm=ÞÝUG[}ý	õ2¼®˜­Ÿû‹j/E2Gå.¿ïC•Å2‘ ýÎÕ•ªA+ªið—Q“•ÞäË
-Õù"å	HQŠ¢˜Ýx ¥Ý£
-6¸(…Ö	PGëaœž„–Õã0pÔö­iˆÒ[¨gžåŒ#ƒÖ®ôq|äõñ‘k`EĉȊt­ˆ¡;¡=”r|´(yV½åz{\žö«yäƒ4~O=‡æõy ^Ú`C°‡è¢æÇHï]Ə	¿øôRÁ¥…œläÁ•Ó¥dî¿’çàŒæÛLæÑÇ–Ý®'¾VÀÙ@­§6ýíõ“RºBh	©«!JÉ…Òg%ã·ž¡\ËËziû®_7`
-‰ œL‡«	tkÌ’Ê"¬KyÀ·&ÀÅÛÛ€c‚H	z?š‘:Ãe7ö¦‰]ÒU$تº“wþõ".sJÜ ±7£ñ{ö—Šê¯-¼ŽÈÄYã“#Š¡sűÒÓÁnëî28€Q—ƒîiÌ!TÈ‘ÏUNÝŽöz8ƒ”/›-nÒêù•——´£óJèzõÐî
-ë GGo
-Å„Låô2(
-8?mó{Þ´ñ†—+¡uzE¿›ºªÝ¿T8/?øG
-Ć‘£&%·Sèæg"ô8z]<[ç‘Þ6d'9=//²LŸ¬\BU¬'´k9@½T;4“d¾À2³oy¸!T{Zñëlúª/¯¹Òˇô”Í̸|g Š{KY-½¤¢Ž'”{‚`öº}-1›ëª×@_®"ÏwËðu„[¿i.Òäͪ
-¾I#}Õ½×¾Áµù`!§¼9UäÜèÁ¬¬˜9ÌÈ6¯B(×uÅUxÙŽ1…xÜÈ‹«ÃA÷07`–¢’è÷£
-]„ŠµHç‡qWàî̸¸1ÌX'UoÁÑü—–Š[¤IW#¡`¦ñT8B6‡˜Ê’ TWº(A'y´xΗ˜V§–L)íCàdXfxsO¡¤·œkí1ä:•ËEDcÛÃxüך+ˆÃÙÙ& è|ùåà»RýÖvûÐÙ2 at M5¯õHýrEÈüç{ÅÅ^̽8M‚}ykMÑ|vKÐ"|ë³~	\´ù\—+,¯™Eš“5
-ha×ïPď/`§òÖc—{Ýæ¯D—ÊNoÖ®ôœРȳt®¥zNÆéIVmýk÷"¼„7/›c’Ÿ/€ðÍ€¡ÊTdY±þœ÷¿Œõwj-5}’éu‰$—~#Ëô¥{‰÷¦ß»<;.÷ñù)»–ª±Pµ9g?RÏ/@uŸ´±q
-6Hs	}ÏŸz‹?.YX¼·Q¸‡´÷p¤Ëi»vK9øc˜Œ´“iëó¥1ü¹ú62ý— ê¤Ó™``’à˜Ï{õŠç§ûþŽ“hv
-endstream
-endobj
-183 0 obj <<
-/Type /Page
-/Contents 184 0 R
-/Resources 182 0 R
-/MediaBox [0 0 612 792]
-/Parent 130 0 R
->> endobj
-185 0 obj <<
-/D [183 0 R /XYZ 99.346 730.572 null]
->> endobj
-57 0 obj <<
-/D [183 0 R /XYZ 100.346 562.185 null]
->> endobj
-61 0 obj <<
-/D [183 0 R /XYZ 100.346 533.535 null]
->> endobj
-65 0 obj <<
-/D [183 0 R /XYZ 100.346 508.526 null]
->> endobj
-69 0 obj <<
-/D [183 0 R /XYZ 100.346 477.938 null]
->> endobj
-182 0 obj <<
-/Font << /F8 129 0 R /F30 128 0 R /F28 125 0 R /F34 186 0 R /F35 187 0 R /F14 188 0 R >>
-/ProcSet [ /PDF /Text ]
->> endobj
-195 0 obj <<
-/Length 2389      
-/Filter /FlateDecode
->>
-stream
-xÚ­YI—ÛƾϯÀóE䋈A7vŸœ8QžíçøEšä"éÐCôÈ€ ƒEôäßžÚ£ÈË…è®Þ«¿úªªx/ðþzÈ÷Ow7·otæ©È£D{wž
-,{I¦ý4J½»Â{¿ùãv§”Ž7ï†ûm¨6ŸðǶ]ÙÔۏwßóÊÏ㘦¼ýL…2ØW2ü§ö`êò?¦Ç»07Íû£å™T2ŸIÅÚÏÃf¤™Îǧª¹7][5Îý,v=[{†‰Õ¦éʾiŸ¸æå~žè{ï´‚óe‘·S™æ<êÎí"f]uàGiþÂæsÆ ¹|ÜlºÒè
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/phylobase -r 701

More information about the Phylobase-commits mailing list