[Phylobase-commits] r754 - pkg/inst/nexusfiles
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Mar 12 17:27:58 CET 2010
Author: francois
Date: 2010-03-12 17:27:58 +0100 (Fri, 12 Mar 2010)
New Revision: 754
Added:
pkg/inst/nexusfiles/treeWithContinuousData.nex
pkg/inst/nexusfiles/treeWithDiscreteData.nex
pkg/inst/nexusfiles/treeWithPolyExcludedData.nex
Removed:
pkg/inst/nexusfiles/treepluscharV01.nex
pkg/inst/nexusfiles/treepluscharV02.nex
Log:
cleaning up of NEXUS files and renamed files to be more explicit
Added: pkg/inst/nexusfiles/treeWithContinuousData.nex
===================================================================
--- pkg/inst/nexusfiles/treeWithContinuousData.nex (rev 0)
+++ pkg/inst/nexusfiles/treeWithContinuousData.nex 2010-03-12 16:27:58 UTC (rev 754)
@@ -0,0 +1,365 @@
+#NEXUS
+[written Tue May 29 18:24:39 PDT 2007 by Mesquite version 1.06 (build g97) at cnidaria-1347.ucdavis.edu/169.237.66.185]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=18;
+ TAXLABELS
+ Myrmecocystuscfnavajo Myrmecocystuscreightoni Myrmecocystusdepilis Myrmecocystuskathjuli Myrmecocystuskennedyi Myrmecocystusmendax Myrmecocystusmexicanus Myrmecocystusmimicus Myrmecocystusnavajo Myrmecocystusnequazcatl Myrmecocystusplacodops Myrmecocystusromainei Myrmecocystussemirufus Myrmecocystussnellingi Myrmecocystustenuinodis Myrmecocystustestaceus Myrmecocystuswheeleri Myrmecocystusyuma
+ ;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Morphology';
+ DIMENSIONS NCHAR=32;
+ FORMAT DATATYPE = CONTINUOUS;
+CHARSTATELABELS
+ 1 eyewidth,
+ 2 eyelength,
+ 3 headlength,
+ 4 headwidth,
+ 5 mesosomaprofilehaircount,
+ 6 FLfemurlength,
+ 7 FLtibialength,
+ 8 MLfemurlength,
+ 9 MLtibialength,
+ 10 HLfemurlength,
+ 11 HLtibialength,
+ 12 mesosomalength,
+ 13 scapelength,
+ 14 funiculuslength,
+ 15 mesosomamaxwidth,
+ 16 mesosomaminwidth,
+ 17 lneyewidth,
+ 18 lneyelength,
+ 19 lnheadlength,
+ 20 lnheadwidth,
+ 21 lnmesosomaprofilehaircount,
+ 22 lnFLfemurlength,
+ 23 lnFLtibialength,
+ 24 lnMLfemurlength,
+ 25 lnMLtibialength,
+ 26 lnHLfemurlength,
+ 27 lnHLtibialength,
+ 28 lnmesosomalength,
+ 29 lnscapelength,
+ 30 lnfuniculuslength,
+ 31 lnmesosomamaxwidth,
+ 32 lnmesosomaminwidth ;
+ MATRIX
+ Myrmecocystuscfnavajo 0.347 0.433 1.338 1.052 39.0 1.434 1.246 1.515 1.409 2.007 2.126 1.962 1.63 2.464 0.836 0.417 -1.058430499 -0.837017551 0.291175962 0.050693114 3.663561646 0.360467742 0.21993842 0.415415439 0.342880233 0.69664107 0.75424228 0.673964361 0.488580015 0.901786046 -0.179126666 -0.874669057
+ Myrmecocystuscreightoni 0.1622 0.20655 0.82985 0.71865 0.0 0.8226 0.68895 0.7854 0.7704 1.0457 1.05835 1.11875 0.89955 1.4073 0.4955 0.28995 -1.819995314 -1.577954034 -0.187439126 -0.332990376 1.098612289 -0.198226599 -0.374805986 -0.242539085 -0.261554411 0.041684897 0.053820826 0.109048315 -0.106449058 0.340231802 -0.70254289 -1.243482504
+ Myrmecocystusdepilis 0.2345 0.279 1.2125 1.0218 24.0 1.25183 1.0856245 1.31244 1.278025 1.70082 1.77591 1.774585 1.335 2.049 0.7741235 0.438396 -1.453769132 -1.2784033 0.185730051 0.015758636 3.163968392 0.217906079 0.073480925 0.262244849 0.23828925 0.523667061 0.565922636 0.566419189 0.284385731 0.712661014 -0.266387722 -0.827757638
+ Myrmecocystuskathjuli 0.206 0.247 1.1235 0.951 19.5 1.35352 1.101125 1.39927 1.29104 1.708335 1.794895 1.70561 1.379 2.04 0.7319725 0.4122135 -1.579985164 -1.398768684 0.115861323 -0.05067484 2.890371758 0.299777539 0.092762585 0.334283576 0.252849066 0.529578184 0.581198779 0.53251657 0.319877422 0.710946449 -0.315164554 -0.88802496
+ Myrmecocystuskennedyi 0.219 0.277 1.2115 1.075 27.5 1.405 1.176 1.4625 1.456 1.8545 1.9205 1.8345 1.4375 2.1 0.7655 0.455 -1.518693975 -1.283737773 0.191857133 0.072285615 3.314020688 0.339154824 0.16141842 0.379143386 0.373863136 0.615804395 0.650805137 0.606659596 0.362132481 0.741737305 -0.267251876 -0.788424862
+ Myrmecocystusmendax 0.2721 0.3336 1.558 1.4531 85.0 1.8742 1.6042 1.994 1.935 2.6013 2.6829 2.5963 1.9381 2.9722 1.0311 0.5232 -1.301585633 -1.097812608 0.443402947 0.373699205 4.442651256 0.628181902 0.47262519 0.690142672 0.660107326 0.95601132 0.986898299 0.954087355 0.661708112 1.089302419 0.030626194 -0.647791479
+ Myrmecocystusmexicanus 0.4335 0.5285 1.602 1.2705 26.5 2.242 1.8555 2.4795 2.2075 3.0705 3.089 2.597 2.211 3.239 0.916 0.394 -0.837335004 -0.642862653 0.466427394 0.227429133 3.275540168 0.796749683 0.612629812 0.902886082 0.785535617 1.116397202 1.124535193 0.952838633 0.792756695 1.172973609 -0.096394475 -0.93952217
+ Myrmecocystusmimicus 0.2197 0.2733 1.141 1.036 30.0 1.23793 1.027 1.26786 1.1749 1.56482 1.63226 1.67201 1.264 1.881 0.708 0.384 -1.5154923 -1.297185186 0.131905071 0.035367144 3.401197382 0.21344063 0.026641931 0.23733044 0.161183038 0.447770801 0.489965558 0.514026496 0.234281296 0.63180355 -0.345311185 -0.957112726
+ Myrmecocystusnavajo 0.2805 0.3755 1.0525 0.795 18.5 1.168535 1.0180075 1.16102 1.12958 1.634705 1.65155 1.546225 1.3485 1.954 0.6263965 0.314671 -1.272519447 -0.980051192 0.050015872 -0.230223916 2.90855558 0.153682711 0.016748671 0.148877742 0.121090106 0.491448376 0.501633856 0.434955774 0.298626416 0.669236464 -0.468766381 -1.171358882
+ Myrmecocystusnequazcatl 0.238 0.295 1.058 1.118 49.0 1.51118 1.1793 1.60672 1.41636 1.95228 1.96042 2.01975 1.477 2.228 0.84806 0.486044 -1.435484605 -1.220779923 0.056380333 0.111541375 3.891820298 0.412890803 0.164921042 0.474194834 0.3480902 0.66899792 0.673158736 0.702973741 0.390013004 0.801104322 -0.164803891 -0.721456124
+ Myrmecocystusplacodops 0.2805 0.347 1.5425 1.4355 39.5 1.6688 1.474045 1.838315 1.761365 2.349265 2.418685 2.28195 1.8045 2.7645 0.955494 0.484641 -1.271539142 -1.058496944 0.433360292 0.360682154 3.675579114 0.512103438 0.387068202 0.606349823 0.563245783 0.852964487 0.881290662 0.824898518 0.589936973 1.015395403 -0.047278511 -0.724537171
+ Myrmecocystusromainei 0.229 0.271 1.164 1.067 27.0 1.31488 1.06962 1.369 1.278 1.74 1.78517 1.72 1.346 2.081 0.797 0.421 -1.474033275 -1.305636458 0.151862349 0.064850972 3.295836866 0.273745407 0.067303445 0.314080546 0.245296356 0.553885113 0.579513649 0.542324291 0.297137231 0.732848547 -0.2269006 -0.865122445
+ Myrmecocystussemirufus 0.2393 0.295 1.3424 1.2826 69.0 1.548 1.3236 1.626 1.611 2.074 2.272 2.0392 1.572 2.3424 0.8935 0.4917 -1.430037284 -1.220779923 0.294459057 0.248889268 4.234106505 0.436963775 0.280355297 0.486123011 0.476855104 0.72947911 0.820660501 0.712557574 0.452348694 0.851176045 -0.112608944 -0.709886505
+ Myrmecocystussnellingi 0.1626 0.2052 0.786 0.69185 17.0 0.7471 0.5778 0.71195 0.68865 0.95225 0.93645 1.02635 0.83555 1.3684 0.47505 0.2805 -1.819869438 -1.586743338 -0.244666624 -0.374320538 2.83148024 -0.296208766 -0.554168612 -0.349125994 -0.38004857 -0.051854551 -0.071457181 0.020580617 -0.182376816 0.309479365 -0.750825896 -1.272022688
+ Myrmecocystustenuinodis 0.16695 0.2165 0.80965 0.69565 15.5 0.82035 0.79215 0.82915 0.7881 1.02385 1.0765 1.0843 0.89445 1.37155 0.5079 0.2895 -1.794140731 -1.531128383 -0.212724354 -0.364765146 2.714672815 -0.201043311 -0.233005565 -0.188002646 -0.240303423 0.023136261 0.071803358 0.077801384 -0.1121299 0.313462769 -0.679348936 -1.244818912
+ Myrmecocystustestaceus 0.271 0.3475 1.0435 0.8825 23.5 1.11074 0.981997 1.145875 1.10783 1.527625 1.55838 1.505275 1.329 2.018 0.6360145 0.288181 -1.305643267 -1.057223576 0.041499168 -0.125900131 3.14578457 0.102786566 -0.021927567 0.135585284 0.099368885 0.423310977 0.441300868 0.408161226 0.283878423 0.701812041 -0.453369253 -1.244254341
+ Myrmecocystuswheeleri 0.197 0.259 1.153 0.981 32.0 1.34961 1.11238 1.43273 1.26582 1.62673 1.75947 1.77914 1.427 2.058 0.732 0.394545 -1.62455155 -1.350927217 0.142367241 -0.019182819 3.465735903 0.299815662 0.106501864 0.359581715 0.235720134 0.486571865 0.565012627 0.576130101 0.355574338 0.721734637 -0.311974765 -0.930022077
+ Myrmecocystusyuma 0.189 0.237 0.864 0.809 10.0 0.867184 0.783 0.878905 0.757646 1.0528 1.15593 1.14947 0.932 1.437 0.549142 0.319 -1.666008264 -1.439695138 -0.14618251 -0.211956362 2.302585093 -0.142504099 -0.244622583 -0.129078464 -0.277539021 0.051453282 0.144905215 0.139300967 -0.070422464 0.362557607 -0.599398219 -1.142564176
+
+;
+
+END;
+
+
+
+BEGIN TREES;
+ TRANSLATE
+ 1 Myrmecocystuscfnavajo,
+ 2 Myrmecocystuscreightoni,
+ 3 Myrmecocystusdepilis,
+ 4 Myrmecocystuskathjuli,
+ 5 Myrmecocystuskennedyi,
+ 6 Myrmecocystusmendax,
+ 7 Myrmecocystusmexicanus,
+ 8 Myrmecocystusmimicus,
+ 9 Myrmecocystusnavajo,
+ 10 Myrmecocystusnequazcatl,
+ 11 Myrmecocystusplacodops,
+ 12 Myrmecocystusromainei,
+ 13 Myrmecocystussemirufus,
+ 14 Myrmecocystussnellingi,
+ 15 Myrmecocystustenuinodis,
+ 16 Myrmecocystustestaceus,
+ 17 Myrmecocystuswheeleri,
+ 18 Myrmecocystusyuma;
+ TREE bestML = (((((((((13:1.724765,11:1.724765):2.926053,6:4.650818):0.689044,(4:1.08387,17:1.08387):4.255993):0.198842,((8:2.708942,3:2.708942):2.027251,((12:2.193845,10:2.193845):2.257581,18:4.451425):0.284767):0.802512):0.506099,5:6.044804):4.524387,2:10.569191):0.836689,(14:2.770378,15:2.770378):8.635503):0.89482,16:12.300701):1.699299,(7:5.724923,(1:2.869547,9:2.869547):2.855375):8.275077);
+
+END;
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED (CHARACTERS = 'Morphology') = Squared: 1 - 32;
+END;
+
+
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 9015005506118934442;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 2565950173085067248;
+ checksum 0 389122022;
+ setID 1 1161953040649633474;
+ checksum 1 3582198254;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #2565950173085067248 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setSize 420 280;
+ setLocation 400 156;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWithCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getWindow;
+ tell It;
+ forceAutosize;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ endTell;
+ showDataWindow #1161953040649633474 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ getTable;
+ tell It;
+ rowNamesWidth 232;
+ endTell;
+ setSize 798 748;
+ setLocation 348 22;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWithCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getWindow;
+ tell It;
+ forceAutosize;
+ endTell;
+ getEmployee #mesquite.categ.StateNamesEditor.StateNamesEditor;
+ tell It;
+ makeWindow;
+ tell It;
+ setSize 314 400;
+ setLocation 60 10;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ setTool mesquite.categ.StateNamesEditor.StateNamesWindow.ibeam;
+ endTell;
+ rowsAreCharacters on;
+ toggleConstrainChar on;
+ toggleConstrainCharNum 3;
+ togglePanel off;
+ endTell;
+ showWindow;
+ endTell;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #9015005506118934442 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 630.1180487973731.4514395117633566598;
+ getTreeWindow;
+ tell It;
+ setSize 520 400;
+ setLocation 60 10;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setEdgeWidth 12;
+ orientUp;
+ getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #1161953040649633474;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 1;
+ toggleShowLegend on;
+ toggleGray off;
+ toggleWeights on;
+ setInitialOffsetX -162;
+ setInitialOffsetY -177;
+ setLegendWidth 142;
+ setLegendHeight 177;
+ resume ;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ endTell;
+ endTell;
+ endTell;
+end;
+
+begin brownie;
+taxset all=1-18;
+end;
Copied: pkg/inst/nexusfiles/treeWithDiscreteData.nex (from rev 744, pkg/inst/nexusfiles/treepluscharV01.nex)
===================================================================
--- pkg/inst/nexusfiles/treeWithDiscreteData.nex (rev 0)
+++ pkg/inst/nexusfiles/treeWithDiscreteData.nex 2010-03-12 16:27:58 UTC (rev 754)
@@ -0,0 +1,354 @@
+#NEXUS
+[written Tue May 29 18:24:39 PDT 2007 by Mesquite version 1.06 (build g97) at cnidaria-1347.ucdavis.edu/169.237.66.185]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=18;
+ TAXLABELS
+ Myrmecocystuscfnavajo Myrmecocystuscreightoni Myrmecocystusdepilis Myrmecocystuskathjuli Myrmecocystuskennedyi Myrmecocystusmendax Myrmecocystusmexicanus Myrmecocystusmimicus Myrmecocystusnavajo Myrmecocystusnequazcatl Myrmecocystusplacodops Myrmecocystusromainei Myrmecocystussemirufus Myrmecocystussnellingi Myrmecocystustenuinodis Myrmecocystustestaceus Myrmecocystuswheeleri Myrmecocystusyuma
+ ;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE Foraging;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2";
+ CHARSTATELABELS
+ 1 time / diurnal crepuscular nocturnal, 2 subgenus / Endiodioctes Eremnocystus Myrmecocystus ;
+ MATRIX
+ Myrmecocystuscfnavajo 22
+
+ Myrmecocystuscreightoni 11
+
+ Myrmecocystusdepilis 00
+
+ Myrmecocystuskathjuli 00
+
+ Myrmecocystuskennedyi 00
+
+ Myrmecocystusmendax 00
+
+ Myrmecocystusmexicanus 22
+
+ Myrmecocystusmimicus 00
+
+ Myrmecocystusnavajo 22
+
+ Myrmecocystusnequazcatl 00
+
+ Myrmecocystusplacodops 00
+
+ Myrmecocystusromainei 00
+
+ Myrmecocystussemirufus 00
+
+ Myrmecocystussnellingi 11
+
+ Myrmecocystustenuinodis 11
+
+ Myrmecocystustestaceus 12
+
+ Myrmecocystuswheeleri 00
+
+ Myrmecocystusyuma 11
+
+
+;
+
+END;
+
+BEGIN TREES;
+ TRANSLATE
+ 1 Myrmecocystuscfnavajo,
+ 2 Myrmecocystuscreightoni,
+ 3 Myrmecocystusdepilis,
+ 4 Myrmecocystuskathjuli,
+ 5 Myrmecocystuskennedyi,
+ 6 Myrmecocystusmendax,
+ 7 Myrmecocystusmexicanus,
+ 8 Myrmecocystusmimicus,
+ 9 Myrmecocystusnavajo,
+ 10 Myrmecocystusnequazcatl,
+ 11 Myrmecocystusplacodops,
+ 12 Myrmecocystusromainei,
+ 13 Myrmecocystussemirufus,
+ 14 Myrmecocystussnellingi,
+ 15 Myrmecocystustenuinodis,
+ 16 Myrmecocystustestaceus,
+ 17 Myrmecocystuswheeleri,
+ 18 Myrmecocystusyuma;
+ TREE bestML = (((((((((13:1.724765,11:1.724765):2.926053,6:4.650818):0.689044,(4:1.08387,17:1.08387):4.255993):0.198842,((8:2.708942,3:2.708942):2.027251,((12:2.193845,10:2.193845):2.257581,18:4.451425):0.284767):0.802512):0.506099,5:6.044804):4.524387,2:10.569191):0.836689,(14:2.770378,15:2.770378):8.635503):0.89482,16:12.300701):1.699299,(7:5.724923,(1:2.869547,9:2.869547):2.855375):8.275077);
+
+END;
+
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED (CHARACTERS = Foraging) = unord: 1 - 2;
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED (CHARACTERS = 'Matrix in file "treepluscharV01.nex"') = Browniandefault: 1 - 32;
+ProbModelSet * UNTITLED (CHARACTERS = Foraging) = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 9015005506118934442;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 2565950173085067248;
+ checksum 0 389122022;
+ setID 1 1161953040649633474;
+ checksum 1 3582198254;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #2565950173085067248 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setSize 420 280;
+ setLocation 400 156;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWithCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getWindow;
+ tell It;
+ forceAutosize;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ endTell;
+ showDataWindow #1161953040649633474 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ getTable;
+ tell It;
+ rowNamesWidth 232;
+ endTell;
+ setSize 798 748;
+ setLocation 348 22;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWithCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getWindow;
+ tell It;
+ forceAutosize;
+ endTell;
+ getEmployee #mesquite.categ.StateNamesEditor.StateNamesEditor;
+ tell It;
+ makeWindow;
+ tell It;
+ setSize 314 400;
+ setLocation 60 10;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ setTool mesquite.categ.StateNamesEditor.StateNamesWindow.ibeam;
+ endTell;
+ rowsAreCharacters on;
+ toggleConstrainChar on;
+ toggleConstrainCharNum 3;
+ togglePanel off;
+ endTell;
+ showWindow;
+ endTell;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #9015005506118934442 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 630.1180487973731.4514395117633566598;
+ getTreeWindow;
+ tell It;
+ setSize 520 400;
+ setLocation 60 10;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setEdgeWidth 12;
+ orientUp;
+ getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #1161953040649633474;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 1;
+ toggleShowLegend on;
+ toggleGray off;
+ toggleWeights on;
+ setInitialOffsetX -162;
+ setInitialOffsetY -177;
+ setLegendWidth 142;
+ setLegendHeight 177;
+ resume ;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ endTell;
+ endTell;
+ endTell;
+end;
+
+begin brownie;
+taxset all=1-18;
+end;
Copied: pkg/inst/nexusfiles/treeWithPolyExcludedData.nex (from rev 748, pkg/inst/nexusfiles/treepluscharV02.nex)
===================================================================
--- pkg/inst/nexusfiles/treeWithPolyExcludedData.nex (rev 0)
+++ pkg/inst/nexusfiles/treeWithPolyExcludedData.nex 2010-03-12 16:27:58 UTC (rev 754)
@@ -0,0 +1,465 @@
+#NEXUS
+[written Wed Mar 10 11:51:23 EST 2010 by Mesquite version 2.72 (build 527) at francois-laptop/127.0.1.1]
+
+BEGIN TAXA;
+ TITLE Taxa;
+ DIMENSIONS NTAX=18;
+ TAXLABELS
+ Myrmecocystuscfnavajo Myrmecocystuscreightoni Myrmecocystusdepilis Myrmecocystuskathjuli Myrmecocystuskennedyi Myrmecocystusmendax Myrmecocystusmexicanus Myrmecocystusmimicus Myrmecocystusnavajo Myrmecocystusnequazcatl Myrmecocystusplacodops Myrmecocystusromainei Myrmecocystussemirufus Myrmecocystussnellingi Myrmecocystustenuinodis Myrmecocystustestaceus Myrmecocystuswheeleri Myrmecocystusyuma
+ ;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE testIncomplete;
+ DIMENSIONS NCHAR=3;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2";
+ CHARSTATELABELS
+ 1 Test1 / test1A test1B, 2 Test2 / test2A test2B, 3 Test3 / test3A test3B test3C ;
+ MATRIX
+ Myrmecocystuscfnavajo 1(0 1)(0 1 2)
+ Myrmecocystuscreightoni ?(0 1)(0 1)
+ Myrmecocystusdepilis 102
+ Myrmecocystuskathjuli 100
+ Myrmecocystuskennedyi 010
+ Myrmecocystusmendax 101
+ Myrmecocystusmexicanus 000
+ Myrmecocystusmimicus ??0
+ Myrmecocystusnavajo ?11
+ Myrmecocystusnequazcatl 100
+ Myrmecocystusplacodops 001
+ Myrmecocystusromainei 11(0 1 2)
+ Myrmecocystussemirufus 001
+ Myrmecocystussnellingi 1?0
+ Myrmecocystustenuinodis 101
+ Myrmecocystustestaceus ??0
+ Myrmecocystuswheeleri 000
+ Myrmecocystusyuma 01?
+
+;
+
+END;
+BEGIN TREES;
+ Title 'Trees from "treepluscharV01.nex"';
+ LINK Taxa = Taxa;
+ TRANSLATE
+ 1 Myrmecocystuscfnavajo,
+ 2 Myrmecocystuscreightoni,
+ 3 Myrmecocystusdepilis,
+ 4 Myrmecocystuskathjuli,
+ 5 Myrmecocystuskennedyi,
+ 6 Myrmecocystusmendax,
+ 7 Myrmecocystusmexicanus,
+ 8 Myrmecocystusmimicus,
+ 9 Myrmecocystusnavajo,
+ 10 Myrmecocystusnequazcatl,
+ 11 Myrmecocystusplacodops,
+ 12 Myrmecocystusromainei,
+ 13 Myrmecocystussemirufus,
+ 14 Myrmecocystussnellingi,
+ 15 Myrmecocystustenuinodis,
+ 16 Myrmecocystustestaceus,
+ 17 Myrmecocystuswheeleri,
+ 18 Myrmecocystusyuma;
+ TREE bestML = (((((((((13:1.724765,11:1.724765):2.926053,6:4.650818):0.689044,(4:1.08387,17:1.08387):4.255993):0.198842,((8:2.708942,3:2.708942):2.027251,((12:2.193845,10:2.193845):2.257581,18:4.451425):0.284767):0.802512):0.506099,5:6.044804):4.524387,2:10.569191):0.836689,(14:2.770378,15:2.770378):8.635503):0.89482,16:12.300701):1.699299,(7:5.724923,(1:2.869547,9:2.869547):2.855375):8.275077);
+
+END;
+
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1 - 3;
+
+ EXSET * UNTITLED = 3;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 3;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ timeSaved 1268239884091;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 9015005506118934442;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 2565950173085067248;
+ checksumv 0 2 4144740407 null numChars 3 short true bits 7 states 7 sumSquaresStatesOnly 220.0 NumFiles 1 NumMatrices 1;
+ endTell;
+ getWindow;
+ tell It;
+ suppress;
+ setResourcesState false false 155;
+ setPopoutState 400;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1278 934;
+ setLocation 1440 0;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ desuppress;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #9015005506118934442 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ suppressEPCResponse;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 630.1180487973731.4514395117633566598;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1123 867;
+ setLocation 1440 0;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ inhibitStretchToggle on;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ centerBrLenLabels on;
+ showBrLensUnspecified on;
+ showBrLenLabelsOnTerminals on;
+ setBrLenLabelColor 0 0 255;
+ setNumBrLenDecimals 6;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleShowFootnotes on;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ namesAngle ?;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ setDrawingSizeMode 0;
+ toggleLegendFloat on;
+ scale 0;
+ toggleTextOnTree off;
+ showWindow;
+ newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #2565950173085067248;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ toggleMPRsMode off;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend on;
+ toggleGray off;
+ toggleWeights on;
+ setInitialOffsetX 4;
+ setInitialOffsetY -191;
+ setLegendWidth 142;
+ setLegendHeight 191;
+ resume ;
+ endTell;
+ endTell;
+ desuppressEPCResponse;
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/phylobase -r 754
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