[Phylobase-commits] r811 - in pkg: . inst/nexusfiles man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Aug 9 03:08:26 CEST 2010
Author: bbolker
Date: 2010-08-09 03:08:26 +0200 (Mon, 09 Aug 2010)
New Revision: 811
Added:
pkg/inst/nexusfiles/treeWithUnderscoreLabels.nex
Modified:
pkg/DESCRIPTION
pkg/man/readNCL.Rd
Log:
changed maintainer e-mail
added note about the fate of underscores in Nexus files
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2010-08-06 19:31:00 UTC (rev 810)
+++ pkg/DESCRIPTION 2010-08-09 01:08:26 UTC (rev 811)
@@ -6,7 +6,7 @@
Depends: methods, grid, ape(>= 2.1), Rcpp (>= 0.8.3)
Suggests: ade4, MASS
Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler, Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
-Maintainer: Ben Bolker <bolker at ufl.edu>
+Maintainer: Ben Bolker <bolker at mcmaster.ca>
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 phylobase.options.R prune.R treePlot.R treestruc.R treewalk.R readNCL.R tbind.R zzz.R
Added: pkg/inst/nexusfiles/treeWithUnderscoreLabels.nex
===================================================================
--- pkg/inst/nexusfiles/treeWithUnderscoreLabels.nex (rev 0)
+++ pkg/inst/nexusfiles/treeWithUnderscoreLabels.nex 2010-08-09 01:08:26 UTC (rev 811)
@@ -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 Myrmecocystus_creightoni 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_period / diurnal crepuscular nocturnal, 2 subgenus / Endiodioctes Eremnocystus Myrmecocystus ;
+ MATRIX
+ Myrmecocystuscfnavajo 22
+
+ Myrmecocystus_creightoni 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 Myrmecocystus_creightoni,
+ 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;
Modified: pkg/man/readNCL.Rd
===================================================================
--- pkg/man/readNCL.Rd 2010-08-06 19:31:00 UTC (rev 810)
+++ pkg/man/readNCL.Rd 2010-08-09 01:08:26 UTC (rev 811)
@@ -107,8 +107,12 @@
\code{missing.data} or \code{extra.data}. See the documentation of
\link{phylo4-methods}, \link{phylo4d} and \link{formatData} for the
complete list of options.
-
+
}
+\note{Underscores in state labels (i.e. trait or taxon names)
+ will be translated to spaces when read by NCL; trait names will
+ be converted to valid R names (see \code{\link{make.names}}) on
+ input to R, so spaces will be translated to periods.}
\value{
Depending on the value of \code{type} and the contents of the file,
one of: a \code{data.frame}, a \linkS4class{phylo4} object, a
More information about the Phylobase-commits
mailing list