[Phylobase-commits] r703 - in www: . misc

[noreply at r-forge.r-project.org]

Author: pdc
Date: 2009-11-01 23:43:49 +0100 (Sun, 01 Nov 2009)
New Revision: 703

Added:
   www/misc/developer.pdf
Removed:
   www/misc/fm-branch.pdf
   www/misc/phylobase_0.3.tar.gz
   www/misc/phylobase_0.3.zip
   www/misc/phylobase_0.3_R_i386-apple-darwin8.10.1.tar.gz
Modified:
   www/index.php
   www/misc/phylobase.pdf
Log:
Update webpage and get rid of old web files

Modified: www/index.php
===================================================================
--- www/index.php	2009-11-01 22:05:50 UTC (rev 702)
+++ www/index.php	2009-11-01 22:43:49 UTC (rev 703)
@@ -33,25 +33,15 @@
 
 <!-- end of project description -->
 
-<h2>How to install phylobase?</h2>
-
-<h3>Current release</h3>
-
+<h2>Package resources</h2>
 <ul>
-<li>You can download the current release version from <a href="http://cran.r-project.org/web/packages/phylobase/index.html">R-forge</a></li>
-<li>Alternatively, you can install it directly within R: <tt>install.packages("phylobase")</tt><li>
+<li>To install the current release version (0.5, rev. 700) use CRAN</li>
 </ul>
 
-<h3>Nightly snapshot</h3>
-
-<ul>
-<li>You can download the <a href="https://r-forge.r-project.org/R/?group_id=111">nighthly</a> snapshot (on a good day) from R-forge.</li>
-<li>You can also install it directly within R: <tt>install.packages("phylobase", repos="http://r-forge.r-project.org")</tt>
-</ul>
-
-<h3>SVN access</h3>
-
-You can checkout the latest version of the source code using <a href="http://subversion.tigris.org/">Subversion</a>:<br/>
+To install the <strong>nightly</strong> snapshot (on a good day, when they build properly) go to <a href="http://r-forge.r-project.org/R/?group_id=111"> the <tt>phylobase</tt> build page.</a>
+<br/>
+<br/>
+The latest version of the source code is always available via <a href="http://subversion.tigris.org/">Subversion</a>:<br/>
 <tt>svn checkout svn://svn.r-forge.r-project.org/svnroot/phylobase</tt>
 
 
@@ -60,18 +50,18 @@
 <tt>phylobase</tt> comes with two vignettes that will help you to get started:
 
 <ul>
-<li><a href="http://cran.r-project.org/web/packages/phylobase/vignettes/phylobase.pdf">phylo4: classes and methods for phylogenetic trees and data</a>
-gives an overview of the tree manipulation and plotting functions available in phylobase</li>
-<li><a href="http://cran.r-project.org/web/packages/phylobase/vignettes/developer.pdf">A developers guide for contributing to phylobase</a>
-provides information about the organization of the package and how to use Subversion.</a>
+<li><a href="http://cran.r-project.org/web/packages/phylobase/vignettes/phylobase.pdf">phylo4: classes and methods for phylogenetic trees and data [pdf]</a>
+gives an overview of the tree manipulation and plotting functions available in phylobase. Also <a href="misc/phylobase.pdf">here [pdf].</a><br/></li>
+
+<li><a href="http://cran.r-project.org/web/packages/phylobase/vignettes/developer.pdf">A developers guide for contributing to phylobase [pdf]</a>
+provides information about the organization of the package and how to use Subversion. Also <a href="misc/developer.pdf">here [pdf].</a>
 </ul>
 
-The best way to get in touch with us is to send an email to our <a href="http://r-forge.r-project.org/mail/?group_id=111">mailing list</a>.
-If you are lucky you can also find us on the <tt>#phylobase</tt> IRC channel at freenode.
-
-<h2>Misc</h2>
+Additional information:
 <ul>
-<li>Peter's 2008 Google Summer of Code <a href="https://www.nescent.org/wg_phyloinformatics/PhyloSoC:Tree_and_data_plotting_in_the_phylobase_project" title="GSOC">project description and progress</a>.</li>
+<li>The <strong>project summary page</strong> can found <a href="http://r-forge.r-project.org/projects/phylobase/"><strong>here</strong></a>. </li>
+
+<li>Much of the plotting code was written as part of the 2008 Google Summer of Code <br/> <a href= "https://www.nescent.org/wg_phyloinformatics/PhyloSoC:Tree_and_data_plotting_in_the_phylobase_project" title = "GSOC"><strong>project description and progress can be found here.</strong></a>. </li>
 </ul>
 
 </body>

Added: www/misc/developer.pdf
===================================================================
--- www/misc/developer.pdf	                        (rev 0)
+++ www/misc/developer.pdf	2009-11-01 22:43:49 UTC (rev 703)
@@ -0,0 +1,3312 @@
+%PDF-1.4
+%ÐÔÅØ
+1 0 obj
+<< /S /GoTo /D (section.1) >>
+endobj
+4 0 obj
+(Introduction)
+endobj
+5 0 obj
+<< /S /GoTo /D (section.2) >>
+endobj
+8 0 obj
+(R-Forge)
+endobj
+9 0 obj
+<< /S /GoTo /D (section.3) >>
+endobj
+12 0 obj
+(Building phylobase)
+endobj
+13 0 obj
+<< /S /GoTo /D (section.4) >>
+endobj
+16 0 obj
+(Coding standards)
+endobj
+17 0 obj
+<< /S /GoTo /D (section.5) >>
+endobj
+20 0 obj
+(Unit testing with RUnit)
+endobj
+21 0 obj
+<< /S /GoTo /D (section.6) >>
+endobj
+24 0 obj
+(Non-exported functions)
+endobj
+25 0 obj
+<< /S /GoTo /D (section*.2) >>
+endobj
+28 0 obj
+(.chnumsort)
+endobj
+29 0 obj
+<< /S /GoTo /D (section*.2) >>
+endobj
+31 0 obj
+(.createEdge)
+endobj
+32 0 obj
+<< /S /GoTo /D (section*.2) >>
+endobj
+34 0 obj
+(.createLabels)
+endobj
+35 0 obj
+<< /S /GoTo /D (section*.2) >>
+endobj
+37 0 obj
+(.genlab)
+endobj
+38 0 obj
+<< /S /GoTo /D (section*.2) >>
+endobj
+40 0 obj
+(.phylo4Data)
+endobj
+41 0 obj
+<< /S /GoTo /D (section*.2) >>
+endobj
+43 0 obj
+(.phylo4ToDataFrame)
+endobj
+44 0 obj
+<< /S /GoTo /D (section*.2) >>
+endobj
+46 0 obj
+(.bubLegendGrob)
+endobj
+47 0 obj
+<< /S /GoTo /D (section*.2) >>
+endobj
+49 0 obj
+(drawDetails.bubLegend)
+endobj
+50 0 obj
+<< /S /GoTo /D (section*.2) >>
+endobj
+52 0 obj
+(orderIndex)
+endobj
+53 0 obj
+<< /S /GoTo /D (section.7) >>
+endobj
+56 0 obj
+(The Nexus Class Library and Rcpp)
+endobj
+57 0 obj
+<< /S /GoTo /D (section.8) >>
+endobj
+60 0 obj
+(S4 classes and methods)
+endobj
+61 0 obj
+<< /S /GoTo /D (section.9) >>
+endobj
+64 0 obj
+(Grid graphics)
+endobj
+65 0 obj
+<< /S /GoTo /D (section.10) >>
+endobj
+68 0 obj
+(Converting between tree formats and ``round-trip'' issues)
+endobj
+69 0 obj
+<< /S /GoTo /D (appendix.A) >>
+endobj
+72 0 obj
+(Subversion)
+endobj
+73 0 obj
+<< /S /GoTo /D (subsection.A.1) >>
+endobj
+76 0 obj
+(Organization of the phylobase repository)
+endobj
+77 0 obj
+<< /S /GoTo /D (subsection.A.2) >>
+endobj
+80 0 obj
+(Using subversion for the first time)
+endobj
+81 0 obj
+<< /S /GoTo /D (subsection.A.3) >>
+endobj
+84 0 obj
+(Subversion patches)
+endobj
+85 0 obj
+<< /S /GoTo /D (subsection.A.4) >>
+endobj
+88 0 obj
+(Branching and merging with svn)
+endobj
+89 0 obj
+<< /S /GoTo /D [90 0 R  /Fit ] >>
+endobj
+116 0 obj <<
+/Length 1148      
+/Filter /FlateDecode
+>>
+stream
+xÚíYÝSÛ8ç¯ðÜÍ=S«ú²$?òQ˜Þ1í
+¤Oô”X$ž;#+@û×ßÊr ‰éBèqÐË–åý­ö§Õj×8G8:ÚÁßi÷;oI‰(Éx48Hž!©òHpŒr]Et˜Ë„ŠØLëY’úÛ$)Ã4ÏË„[W'þ qbE'ˆÐÐZA³É×i=ԍéÆʈ”gõcS¢(â2‹RªÊiø䯄ÊØ8c
 ÷kÿ|å/ºzúöLÕÝÔÓ/íðnðﾑqí&‹žÂÏD.f"»™À‹úüVý[•(W´º§ú`2Â)¨ÏçYøäãÈÕÃ* 1ü&¨E1΃ ªÀPˆqÑ	&£”Sà ‚öë*a$v&4ÿˆÄ`)¸ä. æKÔëú8r”*¼|‚Ú }+˜$iN³ø=Èmí•‹‹ùÈ•€@Âj‰8Ãré¬A Ì¥û8`«…ˆû$=LràÀŽÍS#²€¸7/§EYƒý^2  €ßIùbkeœ#ÉÈÕäAÍýŽ
+¯iÊ‹§«BÛ¢YµÓ¸ ËÕÐñ*d ?U¥XÎ4®LR/À¯J7	w'~­´#×Ô sFÞ\
+ÔøPW©¹žµÓ¯­3E >ŸWíÂlúÀŒ±
¿=TK‚ÿ圃ïµTA£„ªxRùëü¢
5ÖQÁ;c”¤Æ?jx~ß‘ÿÏæ_æ·f3	·D-âÑ}WÊ*=ÖhgÞë»ÆY*¤z¢É¼ ²ž˜—cíãž‚XÛsVEÈ·Ÿ}Óç…n‡—±©¦@J/rd¯nKz*¢¶ä@³‰9pðàÚéuÎÈ+Ú«6œæÖ¹=n	HjÏÐa¢xlõE/qN_äÊ›Ùp><6°£G¶îíiRÑ_¡þ'°PXí½áêÀ8]N›[Rze&^r$ø©á¡¶…±ï«Â\÷ 0¥¯ î>gX+¤‹r9›•!›LLÈ_?˜ë¹¯8A¼ØŸê¦	½ÇåÐjû5<è6åNH\„q'£Ù¬—í&eÌ‘f« Ø) #¯Œé4ÓU—m_7é*w$Ü£BT8²e7¶z6)GýÚebC¨EB†CÆ—þb¬ëÊ*<†LUÆùÒÚUûÒ$ž„ö¥³¦cＶÚ­[é3aÜÖóªH-g¿…βiæ¦é;(“äQFÛMR
JžÎ‡Ki~Tªã×ER–„%YÝ‚vIR)iüÑŽuU~Óm±0õ%˜úÜ·`µ‰¹£¸F@
+¥ß+¨.g±ü¦gͬM&ë¦t5xÊz¾–;Ö]1€oR"D¬žFw
+<|jÂZÃ7°4ÀR—þÒ-–X¼·Ì´=Ÿ1á¶qáÁ•ýãkÎåË(7e[»»ˆ[ŸÞX®x¦](öý^`ö«Œ
aVl…xسº
+¿YûaOf>rÙq×{S·ö¾qYõS…ìE™X®™¸{K”BÜÿSªý½ÑýúYûn°óy‘Áã
+endstream
+endobj
+90 0 obj <<
+/Type /Page
+/Contents 116 0 R
+/Resources 115 0 R
+/MediaBox [0 0 612 792]
+/Parent 127 0 R
+/Annots [ 91 0 R 92 0 R 93 0 R 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 ]
+>> endobj
+91 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
+92 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
+93 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
+94 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
+95 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
+96 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
+97 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
+98 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
+99 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
+100 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
+101 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
+102 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
+103 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
+104 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
+105 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
+106 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
+107 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
+108 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
+109 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
+110 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
+111 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
+112 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
+113 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
+114 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
+117 0 obj <<
+/D [90 0 R /XYZ 99.346 730.572 null]
+>> endobj
+118 0 obj <<
+/D [90 0 R /XYZ 100.346 692.71 null]
+>> endobj
+123 0 obj <<
+/D [90 0 R /XYZ 100.346 535.793 null]
+>> endobj
+115 0 obj <<
+/Font << /F15 119 0 R /F16 120 0 R /F17 121 0 R /F28 122 0 R /F29 124 0 R /F30 125 0 R /F8 126 0 R >>
+/ProcSet [ /PDF /Text ]
+>> endobj
+156 0 obj <<
+/Length 3021      
+/Filter /FlateDecode
+>>
+stream
+xÚµY[ÛÆ~÷¯üPSÀj–ÃáeX4
+Ã.Ü85j/Ž‘rEJb—"e^¼»@|ύ©eÖÞuò"
+g†3ç~¾sè.¶wñ'®üÿxñäü¥gÚWƽÅÅf¡]Ç‹Ðz*ò£ÅEºøàèåJk/p^•K£¶®–+øO»u›WåòãÅ?Ï_ÚE¬âÐñw±ò´²žæ·/vy³\ù¾ç|ηeÖ¶>§ŸÍË¥g6+Ó,噤á	?n»<Íx¸©j^jw2“fŸñõ¬¨ûNŠœ–ª
+SfÜi^d”¡Ë¤v·Eu™4Ù]&O×ô“²'¯¯³ÃrwUMÞVõ-Oò‹•ñzñ„¦â àÚltîÊ|(?ã”U›58$biêPçûÏÃÉ^0uÖ´¼ÜV²Ò>kxfÄ>ƒZN$ŠqGÕî–Ú
ii§_œÉ6˜£µmÅ×ãÑm’òÊÿøï|KlºSþÖZ'D¬ñYEÆY=£«U<XG#³шð²}U÷·mø?)yE˜E£…ÿ´a¬Qd»´ó/ü×5Yý¬?.¡·º¤PLÏÔKVÚøÊ
+êZŞǔyâ&oW/—±ïTõ6û¢s¼éj¼Qì8:Ú±uZ^ÈË
+Ê´oëzw•(ΐJ¬sËóx³5tó^
+žî*ÃOìÃ0qµ¸3õhª82–|ÄÞb½0*ÔA ø0S†"YqÜͦG¤¯‹.%7äÍ8ù®##b³­Ñ‚'.e.…“¿ºÛ ¶²ì
ü€ˆ
+ÈŒkb¢?ÄGÊ4¿
—ՁóıÅšüð«>0CV"7#¢%:ŽÎ×ÎG`Iãå¡3¸°©ºzñx-v*`ˆÉ6ë#ÛLš lÏWËÞãqëpÜe·åÁ Òº•=Çðî,!sšñä:ûÔA`hoAÆ‚sxcòî5 mâ»äÚÙ£!@ór‹sžSä
+rƒCâ÷Í&
ZÈ›u×°‘áÃɃs8»?š#tRn3¹ /e7†2œè5E»+J
i¦/¨ÐS®5cI™{$µ21„Bˆ::PA4¤W48ÚÊűÈÁ Yç±dƐ4]ÖgÈ—ú÷P+£EŸ²BÀºÎ/Ùù¦lW¡°¯ù
óšoÃq䉄×	©æj€	÷¼u
+Ùnýä5Ïž†Kœ{#‰YëHáIT8$u›¯»"A[
+c'ßN“”¤kœløŸ
+
MÆà,Àuè&·—ØNqG³ã
{émBÅï\/éŽ+Ù\õç'-ni½ãJX‰Ü²®öû¼íŽ;ãÊ„£¥0š2_•€
¢mô™~ˆPœ6‰e·vCQ|æ~í°þ
Œ5Ÿg°$Xz¹H¶`ìT¢Kk@—Þ”ß7t¡¢<Dì89òcˉɎŒ,d#ÃÉ™¬‰–èÕ¢`;–£5€ª"C)ÒóH²c–?VÑWÁÒ•	}FójdT6-Çx&Ík0ØB`¦®ösúÀ°¢½žŠ·3† ¼
‡	02Þ˜:í¹P6x„q"Ëÿ¾\€Š„b¾ñ6hONŸžñ.wÕðð;þ{ºkÛÃ_ÏÏëÕU§êÕ¡®þÜ(x|JÙt¡¹ShfšýØåEŠöJ¯@|½bcå[ý5: ÷ŠüÈoñ!!ô\‡²å¥èŽtǐ±ÇdM•âCpÖækaò।c:œsÖâMÉ»ÎÉ>`Tf=IŒÚä&Ùg2Å_q-@ {JÅ!;@`±ÈÐeÆæÞ*Ú{,ÍÓQ¿ž·MVlÚƒùŽ!ßÀ"†AÊéxÝõ€8‚2ü÷u	5ÜHSPÐ
+T#WÑ
+`¼dèÆç—rÌé>/
{ÔI;,ž”	Ã ¾U¾7AKÁ½Ù5Œ§pû•d7ß
+”võTG}#ú!YÁ îÊ’£6€›Ÿ!îÑì›wüÿžÿäÕgd#ð,6#Ò.¼¹KŽá^Vv2Hûšó´<å7&õxÁy±¯l8
Oὂóƒ‰Ü(Y ©¿äezâ¿Ç8Wö.„m梯\Ý¿ÚùJE¹!’41f?kŸ>Z Ú×ʇÅOÑý…Zx‚³…œ	>K{nNIx½’Z'rd~ì+ß÷9ÂÂÑôðíZ¶M^sqÞÝœI,<è…½|ÃSŽBH°ý.)‘ÁSRÔY’ÊÃUÙCJ|ºæ
+£Éû¨K$‘q.–Štžæ8ECf}£¡‘»JÙðš£Õć!íÈœ€æ}#Åæݘ¶hg5ÚtAlCÖóÚ÷yþÅh§E_”­G"…ØÕ÷á@»& 5Ûß“ $	ú0‡ÆVMu3H½n„F­CÈuö^*ý#•ð^Š±2¿ìŽ}–"¿Zñ	„ÄcÙÍã ð|ÌŽJ
+û…NÅ´0¡Rˆá
Å@øÖsO$®^çŸG´Ë{þØ€¹ùT³<êúœþœÿħ½|® ~µ?æ7¾—_kƒ~}3Žyèµà
+o¨ÖÁµ£µÀ†øcoÃôW€+Ž‚ºïMq‚?X™BëÁòÉA¸¯–f2D±ÇÊHm`ÔñICõ”e·ó°É„*îA0€½7mV ÝLËæÇg(ë«ØL2»vOôu§¯èBtÐóÁ­¢¾Øfðú\úî>£À
ñ–iR§ÍÛŒ$,Â> Œ¨Œ	­€4;UÎïdg_éñ…°r¼Ö©²‚és‰HU‰ªú’ºïšœÊì¾î£6p^8Éjÿà
+	>“@N]CÞ `ª³£ê?/nÅw«\×N­mÓ•b ¾õ  ôU!}²°žt045‘žjvUWÈòP™áC^Îá|«©ÔÙÈÄóYœïGʍFe”#€NåRT	ÑÃ]`t->B’¬où©¬ÊÕÀJÝö(Çó xAî˜@Ã.šÔ¦aEﯮöoØÑáÆ 6Œ´óõn
+ã¡Ûƒ°AjbT …M×¢›ÕÃY9««•‰“{I¨°_®:V¼p[	2‘Pu-Ï“,ÆÝ‘pòÉâظål
+—PÃ0„ò dX€ØÑQ­0>ª|Y‡—š\®˜N¶Éeó…ד
XUù€žq@ÄDèÂþ°·À†ÞÐ5Ùly•z<„¿¿­f+>ÔúC…µé—‰c¨¼NZdIÓ êÑ*ÎêiçP$”:`Øón"°MK‰
¦±c•4ò÷ÿÓì†7;ú½éCv`»€D¢°½©æ˜\0Û!¦§›ž4¼3^¸Å×ãï{wOi`ûé$7Ù'$F÷‡Ë?\~lFLÒ°Qž7´Ù(”U;בƒh6¡ŽrC3ø5÷eM{Ê;¶‚½3 r¦qA®v«ž‹!⾸xòé	ŠÊ]èᱧÁÄüh±Þ?ùðÑ]¤°¦XÝ5mÝ/4¶ªbä¼X¼{òoþܬc@ŒqIÇ	*üžkUèN>6ÁMtÌÕ¢aª0PMA•KxZØjƒ•6´Š°IVB}U¯À²mÑ«ú羉„ûêíI†™¹’{B2…Ñ猇‘h&$ôc+$yΨ¯uŽß'®2Œçßoëª;ü–§ßé;©ðw	Õã¯	&¡û$/οGŸ|•ÞøkŸIå[žz‰ë¿ýœ”X­ÒÍ¥|3ë:Á–Ó©V¨èíyZ­AžH\ÓSœ`×IíÚ}ñ@™†ßìEiö
+°¨Y­’áÈòó6[ïʪ@’··ç7ë*ÍC_ôͲ¼¾¾FïÝw5ÈmÇm:îòÕDt"÷m[AArþ@MÛ?Šº¶ÛŠ›¬ÛìæüBŠ¿Y‰½ò+¸ž(¹—(!oŒIŠå+hwÿ £ÏnÚæË65¢UO*…o¡õ:§/Âj³[×k’×e>¯°úíjtTs
+´þŸ`-€ª¹•àÊÚ¹OâcÿÁ»QQ
+endstream
+endobj
+155 0 obj <<
+/Type /Page
+/Contents 156 0 R
+/Resources 154 0 R
+/MediaBox [0 0 612 792]
+/Parent 127 0 R
+/Annots [ 128 0 R 130 0 R 131 0 R 132 0 R 134 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 129 0 R 133 0 R 135 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 ]
+>> endobj
+128 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [323.441 578.786 329.903 591.379]
+/A << /S /GoTo /D (Hfootnote.1) >>
+>> endobj
+130 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [99.35 566.831 155.293 578.786]
+/A << /S /GoTo /D (appendix.A) >>
+>> endobj
+131 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [160.205 566.831 209.05 578.786]
+/A << /S /GoTo /D (appendix.A) >>
+>> endobj
+132 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [137.402 555.429 143.864 567.468]
+/A << /S /GoTo /D (Hfootnote.2) >>
+>> endobj
+134 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [506.623 555.429 513.085 567.468]
+/A << /S /GoTo /D (Hfootnote.3) >>
+>> endobj
+136 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [207.596 543.474 214.058 555.513]
+/A << /S /GoTo /D (Hfootnote.4) >>
+>> endobj
+138 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [494.757 409.113 501.219 419.215]
+/A << /S /GoTo /D (Hfootnote.5) >>
+>> endobj
+140 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [394.213 395.22 400.675 407.26]
+/A << /S /GoTo /D (Hfootnote.6) >>
+>> endobj
+142 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [240.844 383.265 247.306 395.305]
+/A << /S /GoTo /D (Hfootnote.7) >>
+>> endobj
+144 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [339.681 359.147 346.143 371.394]
+/A << /S /GoTo /D (Hfootnote.8) >>
+>> endobj
+146 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [137.264 347.4 143.726 359.439]
+/A << /S /GoTo /D (Hfootnote.9) >>
+>> endobj
+148 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [229.391 335.445 239.824 347.484]
+/A << /S /GoTo /D (Hfootnote.10) >>
+>> endobj
+150 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [343.462 280.702 353.895 292.741]
+/A << /S /GoTo /D (Hfootnote.11) >>
+>> endobj
+129 0 obj <<
+/Type /Annot
+/Border[0 0 0]/H/I/C[0 1 1]
+/Rect [114.593 201.957 278.481 213.454]
+/Subtype/Link/A<</Type/Action/S/URI/URI(http://phylobase.r-forge.r-project.org)>>
+>> endobj
+133 0 obj <<
+/Type /Annot
+/Border[0 0 0]/H/I/C[0 1 1]
+/Rect [114.593 192.453 329.291 203.949]
+/Subtype/Link/A<</Type/Action/S/URI/URI(http://r-forge.r-project.org/tracker/?group_id=111)>>
+>> endobj
+135 0 obj <<
+/Type /Annot
+/Border[0 0 0]/H/I/C[0 1 1]
+/Rect [114.593 182.948 316.589 194.445]
+/Subtype/Link/A<</Type/Action/S/URI/URI(http://r-forge.r-project.org/mail/?group_id=111)>>
+>> endobj
+137 0 obj <<
+/Type /Annot
+/Border[0 0 0]/H/I/C[0 1 1]
+/Rect [114.593 173.444 317.087 184.941]
+/Subtype/Link/A<</Type/Action/S/URI/URI(http://r-forge.r-project.org/R-Forge_Manual.pdf)>>
+>> endobj
+139 0 obj <<
+/Type /Annot
+/Border[0 0 0]/H/I/C[0 1 1]
+/Rect [114.593 163.939 329.291 175.436]
+/Subtype/Link/A<</Type/Action/S/URI/URI(http://cran.r-project.org/doc/manuals/R-admin.html)>>
+>> endobj
+141 0 obj <<
+/Type /Annot
+/Border[0 0 0]/H/I/C[0 1 1]
+/Rect [114.593 154.435 319.827 165.932]
+/Subtype/Link/A<</Type/Action/S/URI/URI(http://developer.apple.com/technology/xcode.html)>>
+>> endobj
+143 0 obj <<
+/Type /Annot
+/Border[0 0 0]/H/I/C[0 1 1]
+/Rect [114.593 144.931 290.685 156.428]
+/Subtype/Link/A<</Type/Action/S/URI/URI(http://www.murdoch-sutherland.com/Rtools/)>>
+>> endobj
+145 0 obj <<
+/Type /Annot
+/Border[0 0 0]/H/I/C[0 1 1]
+/Rect [114.593 135.426 226.675 146.923]
+/Subtype/Link/A<</Type/Action/S/URI/URI(http://www.tug.org/mactex/)>>
+>> endobj
+147 0 obj <<
+/Type /Annot
+/Border[0 0 0]/H/I/C[0 1 1]
+/Rect [114.593 125.922 209.738 137.419]
+/Subtype/Link/A<</Type/Action/S/URI/URI(http://www.miktex.org/)>>
+>> endobj
+149 0 obj <<
+/Type /Annot
+/Border[0 0 0]/H/I/C[0 1 1]
+/Rect [114.593 116.418 325.057 127.914]
+/Subtype/Link/A<</Type/Action/S/URI/URI(http://cran.r-project.org/doc/manuals/R-exts.html)>>
+>> endobj
+151 0 obj <<
+/Type /Annot
+/Border[0 0 0]/H/I/C[0 1 1]
+/Rect [114.593 106.913 298.656 118.41]
+/Subtype/Link/A<</Type/Action/S/URI/URI(http://wiki.fhcrc.org/bioc/Coding_Standards)>>
+>> endobj
+157 0 obj <<
+/D [155 0 R /XYZ 99.346 730.572 null]
+>> endobj
+2 0 obj <<
+/D [155 0 R /XYZ 100.346 692.71 null]
+>> endobj
+6 0 obj <<
+/D [155 0 R /XYZ 100.346 619.813 null]
+>> endobj
+10 0 obj <<
+/D [155 0 R /XYZ 100.346 459.604 null]
+>> endobj
+14 0 obj <<
+/D [155 0 R /XYZ 100.346 321.452 null]
+>> endobj
+161 0 obj <<
+/D [155 0 R /XYZ 115.59 215.257 null]
+>> endobj
+163 0 obj <<
+/D [155 0 R /XYZ 115.59 205.753 null]
+>> endobj
+164 0 obj <<
+/D [155 0 R /XYZ 115.59 196.248 null]
+>> endobj
+165 0 obj <<
+/D [155 0 R /XYZ 115.59 186.744 null]
+>> endobj
+166 0 obj <<
+/D [155 0 R /XYZ 115.59 177.24 null]
+>> endobj
+167 0 obj <<
+/D [155 0 R /XYZ 115.59 167.735 null]
+>> endobj
+168 0 obj <<
+/D [155 0 R /XYZ 115.59 158.231 null]
+>> endobj
+169 0 obj <<
+/D [155 0 R /XYZ 115.59 148.726 null]
+>> endobj
+170 0 obj <<
+/D [155 0 R /XYZ 115.59 139.222 null]
+>> endobj
+171 0 obj <<
+/D [155 0 R /XYZ 115.59 129.718 null]
+>> endobj
+172 0 obj <<
+/D [155 0 R /XYZ 115.59 120.213 null]
+>> endobj
+154 0 obj <<
+/Font << /F28 122 0 R /F8 126 0 R /F30 125 0 R /F7 158 0 R /F32 159 0 R /F16 120 0 R /F19 160 0 R /F31 162 0 R >>
+/ProcSet [ /PDF /Text ]
+>> endobj
+175 0 obj <<
+/Length 3090      
+/Filter /FlateDecode
+>>
+stream
+xÚ•ZY“Û¸~Ÿ_¡ò‹©*Cðf*/ÙìÚåÄåªØãÊÃz«¢03©ð˜#ùó館áL¼/"и>¾ä¯ö+õáÊ—ïO7W×ïƒl¥#FI°º¹]ißÇò*É•Féêf·úÕ‹×­ƒØûV—ýz¦±×Û®/ë=WÊþÀ¥/ëPs¯ßnþvý>[å*O‚'öW›@«,Ð<å?×YèÙõ&ȵgZ)”5ûƒNm…Ì+l×1¥¹åï±Y©wO<}he¬ãŒ'¼mM×·CÑn‘¾™!.CÿŒÍ Ó*Ð)°Kl~q›
™ù*Ëá'à„v·zFú;ˆ3]%*OÃŒ&K”ŽƒU¨ð|:Éø æ"ÒD¯W›³þÀþÑ>¬AM{§Ö›äû´ƒ¢©78ŒÐ™Ja$̐Ç1íÛr;ôeSƒäBí{¦Þqa;ì¹ðÝ×Ñ£•føhï°FIVÔQ{[X&ÅCŠ)Šæx2uiÝ4ÈÕ—V(¡øeƇCYà!¦)¬La:èBÅÛ¡.YSÁL41nÌŸo‰?‹E?²$@ê±³L7pY[UsªÅî`‡{7ÚtVÚ¾û±Oíj/SLÏ¥ƒ9h[»é¶æ„‘xdŸkeÇÍ'Óu(.âB†ØãI6HdPNÔ֥ͶhS¾WÛ½éËûµRpüpÄß-sF]µ÷_n·÷kb—‰Ì-ÒûCÓY&–õi IÐQAu×Ôo{ît4w4š:Ø´U ½ÞÄq2z€é S±_¤u}Ó’z@¹”å—Íìb¯eÝõרD78ëõsï
V¦™³Ê]ÙÚÖBæ!k6ØÆ#¯«q4ÐÛv'!돜‹	½<G!e4ˆÊŽdzßÚŽu qKõXãWkÙ…EÞ—˜/¯’°Á¢vÄÔDvXdÞ‘¶('­C•…ÏÝÑ\:A¦²DÒŸ9-iJoD3a•[Ô**-¬(•íMYuj‰âÿÇ8·9Y‹Öw÷kP"#líÁúØ}adH’ýÇN÷¢‹ÚCCñPh˜}¢Yr^àöѸ‘ÍgÇý }aƒ	¬Žªõåùæb„ãÞÞñT¨`Õ/5²dÍñTÙi5j¦ãHÝq¤r2Ï}¹¯mxÇë΃ñF'©ò“%AF”*‘hüÜ¿}<¡ÿ„Mölx“+êþo¾9ØŽôÓ?´	’\	é¬/dÎxf¶Í}7ö±F'¶Óá©jÀÝÛçLE¹JÇ~uÓó¤´1mM-ˆ¼¯kt\…,{l:é;rË£·g& Â!M@ºI|¡i¶ê,xÉÖ¾“…u¤tO|Jìà °4/
+ÁÀ)j*uè/ÝD®3f@‡z8v°×WÐAœĈ þ‚Ç#˜›	š@9–
+,Xî
+Gì(}‰qõS'¼[ÓË|ØÌ
+kÁ-vÜ…§GË½0ã—ƒWÇô¬ø]ˆNÒã֍ǝÂ@·ÎÑ~jçÎ\¨Ž„xÇÍä¢9[а5Rîä¦ìP…¢ØûëÐŽ'Ä'XÉ7µ+
+;UKåÎN«.ÁE°Ö Õ¼êr¥c§£…@̸åU%e
Õù!ȈAìt¥µ¦·¿ìöv6Ø})´>ïÿÉlAÍ_Q¯<Ìd‡ßHqˆ³~âJ_-—*#‡“r¿VZjk!ÐÁÙÆ™–¸GÑÛ‹`iàxº3ýØØ‹-N_šño¢ŒýãyЭh«ˆè·üy³àÑcéÜ핵ã|Í©'6ã×ó%S€÷Y8ókÑóÂHEùTš-¢'ï_–­Cê}ìyÝ^WÇU߹ͅbs
Eéɲ'¦>í’'Î}ågcÿüíÓ§
+”?ÁŒòVì0Dsƒ¬)šgÑüŒË•• ^iåÎ{[Ûôá•‹'{òšë]Yˆ:àÁÖÑäPR—‘´<‚Ó
èYž:.1š¢Éfá
+gq©‡ÚKŠ%d Ô
kŽj𑿃
+"‡XEÏÙp‘ ñ/Y
+s͝ьN.¥BòÝX)2’ƒÅ/
+ÍšG}×a;Ò&Z›G`#Ž 6	mÞ¼C•É/lÞ–g`ª<±ós^u.J¤ÌžâcÕÔûù(dÄTÕ(õ7âe[7¢âþ58–×}!(h0tîÚ@>ÈËËN-Ò*Æä|Œ™A˜C°«wO\<KÛBD”óA©0Brj˵¹Æãx‚GP€Âú»½ÌÕðwR;éHŠ@iÚÍÁ^°CÖ§•déEB1ùŠ 嘤 í~„$Ý;N4
+wùQ×[îÆñÚµsæ!™i:3IG8³ÈÔ¥Ýi´œ€b²ÈôÒ5 
ö9Ç»KíãíG™YÖPõ\¦¾†?çÞë´|%}¦2_C
+Zf06œÌŽó±(=ù»ÿ–“]š|€„0yäŠUû¥üà‘òÓQÅn›Æ×J)øòUÏ\
Îç“>*çeÁù&Ù¥PPap~µ€5¦&¤‚»à;©*Ö\˜€®¥}
Áø±ÒQ0òt	.P‚†dh¡sÖŒ0<ݾœSüI±8„Ò0Mçû>š;¿”×%ënMû4%^$VC;u]Ξ“Pé0ÿtüatèTÅ:»pI~6½y%³þ7
+Žx9돁ºí°ý†Zï>´Ík0ÍTà¨Ž•*Ö)œ9<$8í‘ö%ä£!eÑÓ%̇¶Ü-Ì!Ä¾5§CYФ	à aPÏ« nÛÃ>äš	j¤,Øc×4߉@º ßWqt
V8ï¶[HË"\Ðj@‘zÄt	|s^ò=ÞS#7Q惃2
+,dû‘IC÷Ð’!…’Pì!>ÇÖL7ÛÊr…÷oMw€~zpĈ–58½žÈe
+Ý|6au¶ÉÅ‹«Bç^3ôœ¶D1;J$¾` ~ t–ϳt–Ö¢ó³»´}”Sà˜¥u¦ å–¥‚œ£Pc`a‡vB|Þ¯
 ›jàk vY„ý:ÉU„g-èdžD30¡ÜÖNÐ/ÈÒ‘:Þ5w…©ø2ϯ±˜[l:׈ HΑÍæ`ÙÊåpÕô†9ᆂ´0®¥a»la†¦˜(q¼¦p÷ÎteAw¥ã]U󪿌R•Æ£+ã{øY®G‡ó\¼xG©ãì¹b¼ê=³Xeúн¸à‹&L’ÏÝ[úg	kŽº¼é<Piž/ìyÁ4,—-D
+Y•töÅ… vÆcè|Ež±Va|æBÙÁƒ€
Fariû]Ñ–â"(	 ø#ú4Ý‘¦¾OHkÉ	ø€­ƒ•@êËÐŒÚ ³ü\UŽyÀ ŽM|…@l2
3™Š|&Tx‚lJ™ì ƒN•ø>`cù¾$Œrï#]»"Ú!¨%|æá½]¥*†Š£ZÅEBË[pf¡1€Â,&ñR2¿\ ó¤ÎòÊõÔu
Ÿ”NΐR:¢(
+F@˜zî[[|ed4åÆ…áë ÌývjÊ–šÀMa¶h8]ä¾â¢°|¢sqT<§9÷âˆ([ëñsŸ©ñ
+ë´ëŒ¥ÈBƒî	²v–¦é8ã<ó~¹¦QœOc™…#³rálÚq@œ–ÛÛbXÌ‚‰ÛÓx§¡m%Ÿbâ}iug‰¼TcadÊ 
X¾«	|gÝ}”ˆ»š…ÝíœÏv4Ža:e[°j ±¿Pa
+ÿ’VÁØÞŁÖVüŒÈo{±€oJ‘%4G3ÞcªÎnÃs‰†BZ ×£ãeëÞ3&1õÊ¡­Ñ}ÿrsõï+|KñWzü«b$áª8^ýú›¿ÚA#lE…y¶z ®GzMHrtžÕêëÕ?øàøc•§©81]L¦3•¸ym‡¥hž»•+áC}¨W¥¾&߬2t+
ø÷P±úþô§ë뢥ëÕnÖ›$Ä?$ pP
+ÐÚýõƒÝ^ŸLq‡OY×ô6vÍ7AöQúcµæ_ˆeY¹
+Ä0R¹ûãEx)½ÿ
E¹/
+endstream
+endobj
+174 0 obj <<
+/Type /Page
+/Contents 175 0 R
+/Resources 173 0 R
+/MediaBox [0 0 612 792]
+/Parent 127 0 R
+/Annots [ 152 0 R 153 0 R ]
+>> endobj
+152 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [406.718 657.993 417.152 670.032]
+/A << /S /GoTo /D (Hfootnote.12) >>
+>> endobj
+153 0 obj <<
+/Type /Annot
+/Border[0 0 0]/H/I/C[0 1 1]
+/Rect [114.593 111.973 349.964 123.47]
+/Subtype/Link/A<</Type/Action/S/URI/URI(http://cran.r-project.org/web/packages/RUnit/index.html)>>
+>> endobj
+176 0 obj <<
+/D [174 0 R /XYZ 99.346 730.572 null]
+>> endobj
+18 0 obj <<
+/D [174 0 R /XYZ 100.346 692.71 null]
+>> endobj
+22 0 obj <<
+/D [174 0 R /XYZ 100.346 572.245 null]
+>> endobj
+26 0 obj <<
+/D [174 0 R /XYZ 100.346 520.536 null]
+>> endobj
+177 0 obj <<
+/D [174 0 R /XYZ 115.59 125.273 null]
+>> endobj
+173 0 obj <<
+/Font << /F28 122 0 R /F8 126 0 R /F30 125 0 R /F7 158 0 R /F19 160 0 R /F31 162 0 R >>
+/ProcSet [ /PDF /Text ]
+>> endobj
+180 0 obj <<
+/Length 2914      
+/Filter /FlateDecode
+>>
+stream
+xڝYKÜ¸¾ï¯ø
+0M‹Ô{rÊ»›
+à8ØÃÚµÄéV¬–:¢Úcùñ©õèÑŒ_ºù(‹Åª¯ª¨ðæpÞüòCxõÿãû^ÿ…7…*R“Þ¼¸Ña¨¢8½Is£²8»y_ßüôCm‡·]m¿Ü~|ÿ×iõëŸóÅÊ$S&O`‚–¼?6îveaðp骱é;ìéÀVeÛښdžþÄ£ãÑâ×2ÅF±ç<X‡é–Ä yy²“ýíÎäA­nwI’oGÙ¤ütÃÖñîåÆŽyªŠ$õ¬Îǯm?Ý0JT˜MöÖèF%Y¼fT?å´‹’Pßì´†á¸ÁÓà_·:°·;Tp€8,‚²«¥
:Ü84݁‡š®nªrä¾fÒDm]3 Æit°2Lºê;èš"¨.Ã`;TÏØ~ŠÎò¢þ>è(>Ë-¼’):;s%?Òôndr¼Š"„«øj?‚Ï·p²½Xì6ø/ùï3]Ÿö`BPˁ™Ð!qn°7ÌüšÆ3ÀITé=ðÿ´ÖÖiJPè—­‰¥¦i0ögl$Ðà=t=Ň0	eñÄ1Ø}Ç£k}–èxp#wDhñÚÝ<%¢Òôã-¼¿´µPÛáÔtåhWIù Ä2ŠHÏQŒÍùŽMk¹éiü]éQ¦ga¡#Áü#j\¤€	V‹,‘µq0ôtKýÈ]\­Ø+LîŽdÈ/L¬Š0ÿ 4Ò1ËžÁÝj“ Ä ·,	~³_.Ž›oÚÒIó×f?”ÃWîË`ã]u>{…˜LeEÁLsaú˜é*ddÝÕj
•Hµ[qÉ™K!\~YqÊó±©ÜÖž:ò7€ŽÀó3þ؁7JrTŽŒ8þxZ¼“¤Fš‡~ #pÜaA¡®7ô—®Þ}œ_ñ`ãv$(ÓdD¦ŠÈ°,îbÝ.	©Ñ*7šI¿—#û‹wôOfz'«š3¸'YŒÌF d徕»èº'Äa_Fžô®–€•ÙSâÅayùSÀ…¤´ù6tkžî©ÐU7xE*Ÿ±{µe"½à¡å€xàslµ
+“¯+ÏöþžÄÜØÀ@D›$¸Ûà€œ«"K×ÞÝ_ªãý=þnðŒU>ïnÇJ±ä±–Àb ÷e…`ò‰{
+XýeäNÛ;²O“d@Wö•;M·—~Bè|†fMÄiÅüÉc‘vÄuŒ<0¹nÐŒƒöKeϘ:8îÏЂV¼““¬ z²4“F¤ͧ3p/`F[éE’ª(Ê¿i1±
+ÃIoˆßÞa¢xi™J³É°Zë6¼Jç*3“áÞÀª)EB±ÇcٱĄ—ØÀÙÉpOøxëO¼_ZðG,{(ÅÏ z›ÚïÖ8ÔÑ+UG)ä}k¥²AG¬P#†hÄ
+õÈî›%7 †Ÿp£}s¸4cCPŠÆ'^ÌP¼ŸG‹C"2„ï2ÎázÂøˆÉ1̓	’ÅkܝsRØßmÅ÷=Z9âk#ÿ§R,;3ŒA§n  ¦Õ¥ÿŒHyIm!§ýÊP;É”ˈ]@;«ǏBtFËÁã0:È »zR‡üƲéìàxN C
Ì‹„¤ø?Ø™ÿië ^W¶m$IXw¼»|}wñ” U³¾(´	
+་øÊ~ÞzÍбxsÓ¥CÓÔ¤_ìp˜ˆ)Õâÿ‹Û.
+•š	$áºòí†Lõ‰û¥FélòwÏ}´˜Ë`ËþûR¶`  q‘ù¿BB5'–&FÚ}3îöd(;h¾bO2=é
+™'ÞhTFÑ(s·3 Q¸K'M¾ó¾µãìÈ『OaG›ª¯	SÊîëÓs›Pé4›âÚo^ÛUvÞ‘þùR1q…æo=ù3·â9ÎÂ]æñf<Ò	´gåµ+:ò·¡Aðå‚žbƒ›DamFiAàÊ°H-—dõ›#T­¡C4¨‹T8/ß(¨ ß('»f]WVraUŒ³`õN¼£ê©4@]=
ËF¬3ê÷îŸ]3ÞßWG[}ú	õâžWÌί}‚Åj/T4Gå.o¿íÃù2‘Q ýÎÌ•oJTCl¸¦ÁQDÃVz¿!_šC¨Î)φ…Êóٍ³î°DÀ†¥PÀâhãFë}c)Q3ºi gíЕ-ê'«ÈH02Ä1•>„ÁGá_^‡x8©4OÖŠpý	í¡Ð‹Xà£EaØ›`²¬ÔãØ“òtx°XÍ#¤éð5÷Í›³ã^š³[°‡èbæǤהñc¯Þ=UpaT®'y rºÐ‚ÁÃ'öd h¾Ku¼íÄýàzÂkœK¨UàÔåpwõ.%+„† KÁÌ’LpðƒÑáõšåñ¨åe½tCߏÏp‰ žLGª	tkÌ’Š<p–RðíVàâíIl€ˆ R‚ޏåÈwُCYL®ù+lUýÉ;ÿš	e®@À‰4êr,ýžÃ¥âúk'¯#òq6Î4æhΙ‘XéÇÁn?7ýÅ‘À,å 5Ï•nÒHes•Ót£=l=œAʗΖ
7iuð£%`öšw$¯„®Wïn° qôÖ­˜ª¼˜^õ¯ÎEÛüÞ†7]zÃËŒŠã+ó_ÎmS5ôD%/äåÿHØ0JÔäävJ=ÁüL„Waƒó$ë=ÒÛ–í$F·Î2}²²ášªÂxB»NÔSµC3ŠæÛ
,+kõ’'BµÐ ~ž?ëKùs®4G}ŸQ$bf%å;ŽGèq,µþý‘‹:~œ0ô!äM÷\b6×Uρ¾^Ežo–áê·~’L%Ñ‹U3|“F†ª)8®}Cj8òÁB*ÎysbعуE!X1K˜Em^eR×åWá	g28Á¦¡™'W‡“ô0ç0K1QðûÑn]„	c•ÌãTàîK·qpc˜±NªÞ£1Î
+^,(îpLS„‚•­7 œÉ90•e%@©nâ«R_¦£,X<çëeN'–L)íÃÆÉ °ÌðFO[Io1×Ú[ƐAêT,™¨Öv‡ñø=†…¼æÊâp[îm»¡èlùåà›RýÖõõÖÙR at M3sz$
+þØrEÈüç{EfÏ	F/N“`_âiT1]ÐjûÖgý¸qÑFes]rØà°¼fiNÖ8L …]¿[@Ã4¾€Ê[]ôº-_‰.•Þ¬©ôÛ83 Až¥+èظ–BÅs2ÎO
+Àµó¯Ý‹ð²½y¾½9b~’?
†)•¦ù÷	s>Ð1ÒÉu
‰C”~#Éô¥{‰ër¨)ÏŽ€Š>þ =g÷@Rµª6“ìGÇóK
ŒV”b@ãlpŒúA>õl<v,>üP²°xoãpiïáÈ—ÓõÝŽsðÏ
+b2ŽÊ®9Cš+O‘«o#Gd	¨/}Áþâ?6\ö‹w‡M,H~b_
+"Jy±Ò²üïÃ
$û?
+ë·³dþŽªÓ%'@H9âg"ÁzW(ä篹P4ѧˆÞ5tn¼-ìàA–£æ`h…ÿ¼™…àÅÿŽ’PEów_H:_	œ\_̲ዠÈӌþÝÙ?‹áÕÜZÏ
+ó®FQšúËàÓ»37Z;|ly¨†ê¿C6\>ëtI1''Uä‰þŽ‚g¯€Z¯¿¥“Å,=ØËî0g±åèÏÙ¶^Wòô¸0a(ßÖÐ
+—ó8©–Ìiþn-^)y¥ÄYùžÎkÎmY­1‰§ÂÁJ|Á xEòÓûþÝæa
+endstream
+endobj
+179 0 obj <<
+/Type /Page
+/Contents 180 0 R
+/Resources 178 0 R
+/MediaBox [0 0 612 792]
+/Parent 127 0 R
+>> endobj
+181 0 obj <<
+/D [179 0 R /XYZ 99.346 730.572 null]
+>> endobj
+54 0 obj <<
+/D [179 0 R /XYZ 100.346 618.207 null]
+>> endobj
+58 0 obj <<
+/D [179 0 R /XYZ 100.346 589.557 null]
+>> endobj
+62 0 obj <<
+/D [179 0 R /XYZ 100.346 564.548 null]
+>> endobj
+66 0 obj <<
+/D [179 0 R /XYZ 100.346 533.96 null]
+>> endobj
+70 0 obj <<
+/D [179 0 R /XYZ 100.346 187.799 null]
+>> endobj
+74 0 obj <<
+/D [179 0 R /XYZ 100.346 161.937 null]
+>> endobj
+178 0 obj <<
+/Font << /F30 125 0 R /F8 126 0 R /F28 122 0 R /F34 182 0 R /F35 183 0 R /F14 184 0 R /F16 120 0 R >>
+/ProcSet [ /PDF /Text ]
+>> endobj
+191 0 obj <<
+/Length 2675      
+/Filter /FlateDecode
+>>
+stream
+xÚ­YÉ’ÛȽ÷W æ"0<Q…}N–5’CvH3nµ}‘怪I¸A€Æ"ª/þvçV A²eYãQû’õòåBßÙ:¾óçÿìû§»›Í› r2/‹uìÜ=8JEžÎ´§ÚKÂĹ+î'­üÕow™æÁ$ÿd–tÐàÃãvƒƒ7oÒ“!:òTh‡w¦3«u¨CwØQ!p÷yÕHS7®”Û<r­}à~º‡®]­£Èý§)n1_ª~è½Õ:Q‘{·«zžQVi»'e›ïǪ–‰ySr[¾Ò©ûy«æUß×/à¬ùÐk¥¼,ŠøèîkÇínµ9S„îíúÍ*…³v[i¨š~È뚇íMëïò¦ê÷Üß·ÜU
+òíeÞþ°ZëVò'
+Ü>ìòa9ã÷½éYЋÇTè¥aje}ÂÒ‘ûêÝÏ\(v¦x<ÌS¬
+øÜuôòm
+™&Áð.E{¨ŒH ß›î×™ÏU;^»¡ò3Oû3àvOu{Ÿ÷ærÇÈ÷‚l‚]gj“÷v£Üîþˆr6‡á«BQYæùÚ
+%þ¡Çk2	¼Ôm)¥Œ-,¶Á6W sÈmÃCÛqá°Ã«XiP¿û|µVn…Š…ÓÐ6S‚Ê„•ÑYæîqþØ<ç> ®LR¢iŽ=&ë
+_d©,íE\›ÏthQ:0w#jùq>ù*ij–¢KN§¯¯éQ ¨™ŸÀ7ñÒ4å=_znª éï«fó“ÈíÇûU @ÃáÇt}Õ6Ü΁k2pã@­Õþ
+¨|¸d
+¸âýîhf¸[Ó˜.dž…Úp_b”ÝڏØÐv\ƒ=£[Ž²RK`ðÅzY¯ç®‡¶®y(ò]˜h÷í-;vÕ0Ùe w¥ýªaÇöy!muE3~ájÕÈ€ª)¤'õ—¹“#2$”½ÌŠ#Ø )å\Ü0öp_,ÆÐGDG'§ç:K†ôùÞÈB³dâÈJ&±îǁ`Ÿ¦Í¸órÛ.U ¸xÐÜîÞµ¥BÕ ¸®\sÂæüv‰¼ÝæêQ„€Ð¼câÚª7þñÞ>ðAàÉÇÔ>:M¶HœØË’ %V¨×	¼XÉYTpÆ.é‚’4 0…oäEb¨—ú”a›à‚õ˜–tºán!ƒ‘“²c¥ÀKïØlñeKîhé
²á
+ƒ€L7”<Z 46É:x Ù'Äm¶÷Mj
+ýÌ}¢Geï¼á-¶Ff3L°KN/”†.ÏìsÞð#?íÁv>àÐŸè'þÛZ“ÊFÖ7 >¯­1Úï	6
+.Z¼À3<Òp%ÔnNl-‰kŸT^Cÿi³_¯[?àÓÁðþUìéÚvØ|ÅÎYIœžâí²ˆž…«%/5Ö%Wg(ãÈ¡åÖ}þ(”‚5”G5ô<„}*”ëé¶UÐзcWȼÎèµÚ¾b'ìâ01åéBælÁ•CR¡Ã"k=ûÒK¬‡b“‚092¶–%Šõp²Yç^Eà{¡ÒßæUD@ÿvàì"l>vʆ !ËtY·,Ó!}§©ûKSÈAE4/>¯æ×mc왫ù'šdøX•…“©Dj)–m€¦¾åï.ŸéLzvRèû
+OÒJú…ñÀ_ÒyøÊ
:®-ß
õ¼(Ú‘µ/	¶ldo÷œu
+jˆ-x¶žkb( DD)œª‹8](QLv =çyN³A¬MIö	ʨ{ï覎4Ô0³¶«ÈÏ´x59´6-ÌC¹°%[CËG"²»|0³Å„–9:¹B	3!ž:ª´X€þBäÛ²e1ù|Ô/Dsp@h7›WmyÜ:öT4iÁ°—»ÇFa…ÌhÃœgvŠ´—‚I’5>6`Ý»Ü)P`¾æ–à	Æ®ù‰è^à²Þ·ÐóZƒsƒñ]ðcQ2-ÿ›±y†™ÿG"ÿ¨9_ùÿwN¶ˆü„@eRm&hÉùs¢$P#%/c6̳¨õQl1…°š YV²^_¾"ݧ™Bo%_V#,”%{Ý0èalŠ
ü¦þlLÉf¼÷¦Y?OðCŽ“)FÉÜ´ûtE•º6¦Þr…Ci¦9í3r;j"`©t¦¨eàäu²Ü,Ph>¨’p»jPdŠÔ¹_
+$a$£Ó«¬ XjŠ‚³+0j؃?M0ÌÊ=gÀՁþŽ\´ËûÙ­ÁØ@"ª|Òi"7wU--8ˆÝ~KDÖI‡—ö~4Jæ·Aÿ35äø3@Š¥¡”„íÞp÷ÀÐjké!žÆŽ"*tí¶<âì…(¤	KO<`gê¯a†mDÏ€ý’˜ŠÎW’}ó†‡ÝKL÷,Ü%eÄÎJ`½™)õ’3o›$æiœ<74œªY`Ò!žµ³A¤øG6L$‰¢É£™€<ùÐæEЋ[ìyá×aoQ¸èU0#Ô£멦+A3Û6h*:“38¡µ;&e÷UåíJn#—¯iúž;OˆNÙ¸R…çǽ“_ $úQ8bÓoçcD\ %sí†ÝØ4|ÚYaÏ"¨ïQ’âÀ:²¾]˜©É`l(Ïzµk
+׸jÏ®çŸ]ãÛóMõSAÚå„%:úª™®k»ž;8=¥%
+ìPZÒÃ@ÀRA*Œ3Dz¤ïÛ“ž¹âlhL+êä¿æ;—7‰ÁÙc;)—ó4†!> {²>Š“<8à–ÏXX,ÀAC/UÉRΗdŒëÇñÄ^‡–¸dŒa1uíY|c^A‡^ªE!üJ
Žìg
ÜaÏ©DLÚtÕ@¨ÆÊ-Ÿôõ0L=tlF?ôœ>Ñ_”v“.O².ºJX°ç6Žã’"/
+.âû’s÷Ï1]ÈÞù>—÷Ýô϶Äàõò€ýBtœnŒuKôáDôáE€&FØ'®å†‘J¦3ûÇ%nÏšŸ_xuûö×»·¿¼¿ŠVÌhåÌÕ¹{ŸzÉœë~ÿòÝ뿾|õúr±0ÄFvàDÌèŸU.‰ÙÔÙl	6ˆ¦ÚT)ž{
^qÆ…ŠÍÙ¼…ÑÒœ……çò®Ü‰r\i}]
+Myi<…;ìÂ2ùl,;…˜ ,H¦ï‰ka<Œ5—Ù‹€ú“óÄ$¼-f—x˜óc8òÈ°	äÞX¨ú~œŠˆMp‘_J²uÒÐ×w7ÿºÁÿ|G9Ê÷½ XJ‰‡N±¿ùø›ï”ÐÔîËiäÞQqèÅ>jí|¸ùÿ±§2'rHäO“ÄKÒ˜ÒY–.Œ°­óèØRK œ¦û
+§'^ê#ñtÉÃ
Bð
 ¦?1ܪm·ÃçŒy§YËz1œZ-¨ê÷œ¥è(i±Öj“wÄ
>ÐvS¶ÅX¶ßÜâíš/À‡òáª}~†4ÓÔƒ÷ Ö„chÞ>:Âÿ *`ƒs
+endstream
+endobj
+190 0 obj <<
+/Type /Page
+/Contents 191 0 R
+/Resources 189 0 R
+/MediaBox [0 0 612 792]
+/Parent 127 0 R
+/Annots [ 185 0 R 187 0 R 186 0 R 188 0 R ]
+>> endobj
+185 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [242.674 545.865 253.107 557.904]
+/A << /S /GoTo /D (Hfootnote.13) >>
+>> endobj
+187 0 obj <<
+/Type /Annot
+/Subtype /Link
+/Border[0 0 0]/H/I/C[1 0 0]
+/Rect [224.09 178.686 234.524 191.279]
+/A << /S /GoTo /D (Hfootnote.14) >>
+>> endobj
+186 0 obj <<
+/Type /Annot
+/Border[0 0 0]/H/I/C[0 1 1]
+/Rect [114.593 124.35 243.611 135.847]
+/Subtype/Link/A<</Type/Action/S/URI/URI(http://tortoisesvn.tigris.org/)>>
+>> endobj
+188 0 obj <<
+/Type /Annot
+/Border[0 0 0]/H/I/C[0 1 1]
+/Rect [114.593 114.845 320.823 126.342]
+/Subtype/Link/A<</Type/Action/S/URI/URI(http://cran.r-project.org/doc/manuals/R-exts.pdf)>>
+>> endobj
+192 0 obj <<
+/D [190 0 R /XYZ 99.346 730.572 null]
+>> endobj
+78 0 obj <<
+/D [190 0 R /XYZ 100.346 603.108 null]
+>> endobj
+193 0 obj <<
+/D [190 0 R /XYZ 115.59 137.65 null]
+>> endobj
+194 0 obj <<
+/D [190 0 R /XYZ 115.59 128.146 null]
+>> endobj
+189 0 obj <<
+/Font << /F35 183 0 R /F30 125 0 R /F8 126 0 R /F28 122 0 R /F7 158 0 R /F19 160 0 R /F31 162 0 R >>
+/ProcSet [ /PDF /Text ]
+>> endobj
+199 0 obj <<
+/Length 1948      
+/Filter /FlateDecode
+>>
+stream
+xڥˎãDð>_a–Ã8éq»ýÊ
+	-â ;h»»“˜øìöfGˆ§Ýv2“a9$ýªª®®w9ð¶^à}ØñÛû›»×™·«$L¼û'ƒ@¨(ñ’,i”z÷¥÷Þ7;½X*úE×4y[.~¿ÿñîµ
+Nð’PÈ0š„pè»æ`>q ?É৷D‘XÅ‘ƒ>VuÍô
ofþǪ¤•ÿAªèC £º^VíøX®ë¼Ý¿`ð²[,
¼Ý"žÉMÕµ|Vmx|X„©ß·é÷–è´ªÝ2pŽ¬zK¤"HW0‘ÀgÌ\nƶ°ä•ò7]“È7@˜Äsä´C˜ªÑ‚èIxmS»'œ0ñ[ýÉðl0ú€³Ô¯€æÀSÓñ¡É÷ȪEÊy¨ù!ÝÞîZBÇÏRÿH8·OQ3æuýÀ«¥³ƒëòv«K±XFQèß/–’6õE«@
+'NwÈ|žjXE"Q¡ƒrvÃ졺IÎ*Ä
+ Î$3ìÈŽ ÇÀrøÀ²Ís¼x¾&1hÝZœ²Ô¥ÃˆƒQ,²tbïÕSþc*wŒ6üÓkXâe…¬üË%1ùtÇÏWßA–ce_7¶û–EBïKè>‹ôK^79žZµÚ±E¦3KçD6Î)½e’3g›‰u÷Ž-x×(|¶ž~˜lÿ™÷& r¹rúæò{åéƒÉ=¦XäÆGd—ÉJd1²*ÀTØD>'q?k}ÎãNp^/2Å¢M!8´€ÙÚ®6<¾AGI}»ë¬§<´2U³Âf
Îäà6Öů¼&
f>SuL§¸¥‡öÖ8̺žÌY2|ÓhTm9äÁh
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/phylobase -r 703