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| /* PDAP:PDTREE package for Mesquite copyright 2001-2009 P. Midford & W. MaddisonPDAP:PDTREE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.The web site for PDAP:PDTREE is http://mesquiteproject.org/pdap_mesquite/This source code and its compiled class files are free and modifiable under the terms of GNU Lesser General Public License. (http://www.gnu.org/copyleft/lesser.html) */package mesquite.pdap.RootedRegression;/*~~ */import mesquite.lib.*;import mesquite.lib.characters.*;import mesquite.cont.lib.*;import mesquite.pdap.CIReport.CIReport;import mesquite.pdap.SPRootRegression.SPRootRegression;import mesquite.pdap.lib.*;/* ======================================================================== */public class RootedRegression extends RootRegressionCalculator { public void getEmployeeNeeds(){ //This gets called on startup to harvest information; override this and inside, call registerEmployeeNeed EmployeeNeed e = registerEmployeeNeed(SPRootRegression.class, getName() + " needs a method to calculate correlations.", "The method to calculate correlations is selected initially"); EmployeeNeed e2 = registerEmployeeNeed(CIReport.class, getName() + " needs a method to generate CI reports.", "The method to generate CI reports is selected initially"); } Tree myTree = null; TreeReference lastTreeReference; String DiagnosticString; PDAPRootRegStatPak myStats = null; StatPakSource sp2cts; MesquiteChart chart; PDAPTreeWinAsstC chartModule = null; CIReport CIReportTask; ContinuousDistribution observedStates1 = null; ContinuousDistribution observedStates2 = null; /*.................................................................................................................*/ public boolean startJob(String arguments, Object condition, boolean hiredByName) { lastTreeReference = null; addMenuItem("Root Calculation Query Mode...", makeCommand("setVerboseQueryMode", (Commandable)this)); addMenuItem("Set CI/PI width...", makeCommand("setwidth", (Commandable)this)); addMenuItem("Set Vh...", makeCommand("setvh", (Commandable)this)); addMenuItem("Set Polytomy DF Reduction...", makeCommand("setDFReduction", (Commandable)this)); addMenuItem("Ignore Root Tritomies...", makeCommand("setIgnoreRootTritomies", (Commandable)this)); addMenuItem("Show CI/PI columns (text window)",makeCommand("showCIPIColumns", (Commandable)this)); addMenuItem("Add a value to the CI/PI table",makeCommand("addCIPIvalues",(Commandable)this)); addMenuItem(null, "Write CI/PI table to a file", makeCommand("writeCI", (Commandable)this)); sp2cts = (StatPakSource)hireNamedEmployee(SPRootRegression.class, "#SPRootRegression"); if (sp2cts == null) return sorry(getName() + " couldn't start because no calculator of correlation obtained"); //myStats = sp2cts.getStatPak(); CIReportTask = (CIReport)hireNamedEmployee(CIReport.class, "#CIReport"); if (CIReportTask == null) return sorry(getName() + " couldn't start because no CI reporter module obtained."); return true; } /*-----------------------------------------*/ public Snapshot getSnapshot(MesquiteFile file) { if (myStats == null) return null; if (myStats.getCIPIValuesSize()==0) return null; final Snapshot temp = new Snapshot(); for(int i=0;i<myStats.getCIPIValuesSize();i++) temp.addLine("addCIPIvalues " + myStats.CIPIValueAt(i).toString()); return temp; } /*-----------------------------------------*/ /** * This just generates the description of the columns in the CI/PI file. It's * broken out to make doCommand easier to follow. * @return String the columns' description */ private String makeCIPIcolumnString() { double width1 = 0.95; double width2 = 0.90; if (myStats != null) { width1 = myStats.getWidth1(); width2 = myStats.getWidth2(); } final String width1percent = MesquiteDouble.toString(width1*100); final String width2percent = MesquiteDouble.toString(width2*100); return("The Confidence and Prediction interval (CI/PI) value dump on the text pane contains the following columns:\n\n" + " 1. Tip Name\n" + " 2. X Value\n" + " 3. Observed Y Value (or -99999 for generated X values)\n" + " 4. Predicted Y Value (Yhat)\n" + " 5. Lower " + width1percent + "% Confidence Interval\n" + " 6. Upper " + width1percent + "% Confidence Interval\n" + " 7. Lower " + width1percent + "% Prediction Interval\n" + " 8. Upper " + width1percent + "% Prediction Interval\n" + " 9. Lower " + width2percent + "% Confidence Interval\n" + "10. Upper " + width2percent + "% Confidence Interval\n" + "11. Lower " + width2percent + "% Prediction Interval\n" + "12. Upper " + width2percent + "% Prediction Interval\n"); } /** * The dispatcher for mesquite/script commands */ public Object doCommand(String commandName, String arguments, CommandChecker checker) { if (myStats == null) return null; final Class thisClass = this.getClass(); if (checker.compare(thisClass,"Sets the first width for the confidence and prediction intervals","[a confidence width e.g., 0.95]",commandName,"setwidth1")){ double newWidth= MesquiteDouble.fromString(arguments, new MesquiteInteger(0)); if (!MesquiteDouble.isCombinable(newWidth)){ chartModule.queryWidths(); newWidth = chartModule.getWidth1(); } myStats.setWidth1(newWidth); chartModule.setWidthQueryDone(true); parametersChanged(); } else if (checker.compare(thisClass,"Sets the second width for the confidence and prediction intervals","[a confidence width e.g., 0.90]",commandName,"setwidth2")){ MesquiteInteger pos = new MesquiteInteger(0); double newWidth= MesquiteDouble.fromString(arguments, pos); if (!MesquiteDouble.isCombinable(newWidth)){ chartModule.queryWidths(); newWidth = chartModule.getWidth2(); } myStats.setWidth2(newWidth); chartModule.setWidthQueryDone(true); parametersChanged(); } else if (checker.compare(thisClass,"Sets both widths for the confidence and prediction intervals","[two confidence widths e.g., 0.95 0.90]",commandName,"setwidth")){ MesquiteInteger pos = new MesquiteInteger(0); double newWidth1= MesquiteDouble.fromString(arguments, pos); MesquiteInteger pos2 = null; double newWidth2 = MesquiteDouble.unassigned; if (MesquiteDouble.isCombinable(newWidth1)) { pos2 = new MesquiteInteger(arguments.indexOf(' ',0)); if (pos2.getValue()>0) newWidth2 = MesquiteDouble.fromString(arguments,pos2); } if (!MesquiteDouble.isCombinable(newWidth1) || !MesquiteDouble.isCombinable(newWidth2)){ chartModule.queryWidths(); newWidth1 = chartModule.getWidth1(); newWidth2 = chartModule.getWidth2(); } myStats.setWidth1(newWidth1); myStats.setWidth2(newWidth2); chartModule.setWidthQueryDone(true); parametersChanged(); } else if (checker.compare(thisClass,"Sets the tip to root distance for added nodes in prediction interval regression estimates","[a real number]",commandName,"setvh")) { MesquiteInteger pos = new MesquiteInteger(0); double newVh= MesquiteDouble.fromString(arguments, pos); if (!MesquiteDouble.isCombinable(newVh)) myStats.setVh(chartModule.queryVh(myStats)); else myStats.setVh(newVh); parametersChanged(); } else if (checker.compare(thisClass,"Sets the degrees of freedom reduced because of polytomies","[number of dof]",commandName,"setDFReduction")) { MesquiteInteger pos = new MesquiteInteger(0); int dfReduction= MesquiteInteger.fromFirstToken(arguments, pos); if (!MesquiteInteger.isCombinable(dfReduction)) chartModule.queryDFReduce(myStats, true); else chartModule.setDFReduction(dfReduction); chartModule.setDFQueryDone(true); myStats.setDFReduction(chartModule.getDFReduction()); parametersChanged(); } else if (checker.compare(thisClass, "Sets the query mode to verbose or not", "[on/off]", commandName, "setVerboseQueryMode")) { if (StringUtil.blank(arguments)) chartModule.queryVerboseQueryMode(); else chartModule.toggleVerboseQueryMode(parser.getFirstToken(arguments)); } else if (checker.compare(thisClass,"Sets whether to ignore a tritomy at the root ", "[boolean]",commandName, "setIgnoreRootTritomies")){ if (StringUtil.blank(arguments)) chartModule.queryIgnoreRootTritomies(); else{ String s = parser.getFirstToken(arguments); chartModule.setIgnoreRootTritomies("on".equalsIgnoreCase(s)); } myStats.setIgnoreRootTritomies(chartModule.getIgnoreRootTritomies()); } else if (checker.compare(thisClass,"Write CI/PI table to a file",null,commandName,"writeCI")) { CIReportTask.setStatPak(myStats); MesquiteFile CIfile = new MesquiteFile(); CIReportTask.writeReport(CIfile,observedStates1,observedStates2,myTree,arguments); } else if (checker.compare(thisClass,"Show CI/PI columns (text window)","",commandName, "showCIPIColumns")){ String description = makeCIPIcolumnString(); AlertDialog.notice(null,"CI/PI Columns",description); } else if(checker.compare(thisClass,"Add a value to the CI/PI table","[a real number]",commandName,"addCIPIValues")) { double newValue; if (StringUtil.blank(arguments)){ newValue = MesquiteDouble.queryDouble(null,"Add CI/PI value","Enter x (horizontal trait) value to add to the CI/PI table",0.0); } else{ MesquiteInteger pos = new MesquiteInteger(0); newValue = MesquiteDouble.fromString(arguments, pos); } if (MesquiteDouble.isCombinable(newValue)) myStats.addCIPIValue(new MesquiteDouble(newValue)); } else return super.doCommand(commandName, arguments, checker); return null; } /*-----------------------------------------*/ public void setChartModule(PDAPTreeWinAsstC module) { chartModule = module; myStats = (PDAPRootRegStatPak)sp2cts.getStatPak(); myStats.setDFReduction(chartModule.getDFReduction()); myStats.setIgnoreRootTritomies(chartModule.getIgnoreRootTritomies()); } /*-----------------------------------------*/ public PDAPRootStatPak getStatPak() { if (chartModule == null){ MesquiteMessage.warnProgrammer("No chartModule set for "+this); return null; } if (myStats == null){ myStats = (PDAPRootRegStatPak)sp2cts.getStatPak(); myStats.setDFReduction(chartModule.getDFReduction()); myStats.setIgnoreRootTritomies(chartModule.getIgnoreRootTritomies()); } return myStats; } public void setChart(MesquiteChart chart){ this.chart = chart; } /*.................................................................................................................*/ public void calculateNumbers(Tree tree, CharacterDistribution charDistribution1, CharacterDistribution charDistribution2, NumberArray result, MesquiteString resultString) { if (result==null || tree == null) return; if (!(charDistribution1 instanceof ContinuousDistribution) ||!(charDistribution2 instanceof ContinuousDistribution)) return; clearResultAndLastResult(result); result.zeroArray(); observedStates1 = (ContinuousDistribution)charDistribution1; observedStates2 = (ContinuousDistribution)charDistribution2; if ((lastTreeReference == null) || (tree instanceof MesquiteTree && !((MesquiteTree)tree).sameTreeVersions(lastTreeReference, true, true))) { // Peter: tighter restrictions; any change will provoke query or reset // first create and initialize the new rootStatPak myStats = (PDAPRootRegStatPak)sp2cts.getStatPak(); myStats.setDFReduction(chartModule.getDFReduction()); myStats.setIgnoreRootTritomies(chartModule.getIgnoreRootTritomies()); // now set the tree so doCalculations will do the right thing... myStats.setTree(tree); final int root = tree.getRoot(); myStats.countInternalNodes(tree,root); // count the internal nodes, to set number int zlb = ((NoPolyTree)tree).countZLBs(myStats.getIgnoreRootTritomies()); // Zero-Length-Branches are what PDAP calls "polytomies"; count to inform the user // now ask the user to set df Reductions if (!MesquiteThread.isScripting()){ if (!chartModule.getDFQueryDone() && ((zlb > 0) || chartModule.getVerboseQueryMode())){ chartModule.queryDFReduce(myStats,true); myStats.setDFReduction(chartModule.getDFReduction()); chartModule.setDFQueryDone(true); } if (chartModule.getVerboseQueryMode() && !chartModule.getVhQueryDone()){ chartModule.queryVh(myStats); myStats.setVh(chartModule.getVh()); chartModule.setVhQueryDone(true); } else{ myStats.setVh(myStats.getMeanHeight(tree)); } if (chartModule.getVerboseQueryMode() && !chartModule.getWidthQueryDone()){ chartModule.queryWidths(); myStats.setWidth1(chartModule.getWidth1()); myStats.setWidth2(chartModule.getWidth2()); chartModule.setWidthQueryDone(true); } } else { myStats.setDFReduction(chartModule.getDFReduction()); myStats.setIgnoreRootTritomies(chartModule.getIgnoreRootTritomies()); myStats.setWidth1(chartModule.getWidth1()); myStats.setWidth2(chartModule.getWidth2()); myStats.setVh(myStats.getMeanHeight(tree)); } } myTree = tree; lastTreeReference = ((MesquiteTree)tree).getTreeReference(lastTreeReference); if ((observedStates1 != null) || (observedStates2 != null)) { NumberArray xArray = new NumberArray(); NumberArray yArray = new NumberArray(); myStats.setObserved1(observedStates1); myStats.setObserved2(observedStates2); boolean munch = myStats.doCalculations(xArray,yArray,chart); // Results are never set - we just leave the tip data untouched for display if (resultString == null) MesquiteMessage.warnProgrammer("RootedRegression should NOT be called with an empty result string - uncontrolled recursion may occur"); else { if (munch) resultString.setValue("Needs remunching"); else resultString.setValue("CI and PI around Regression through root"); } } saveLastResult(result); saveLastResultString(resultString); } /*.................................................................................................................*/ /*.................................................................................................................*/ public Class getCharacterClass() { return ContinuousState.class; } /*.................................................................................................................*/ public CompatibilityTest getCompatibilityTest() { return new ContinuousStateTest(); } /** returns current parameters, for logging etc..*/ /*.................................................................................................................*/ public String getParameters() { return "Regression through reconstructed root"; } /*.................................................................................................................*/ public String getName() { return "Regression through Reconstructed Root Value"; } /*.................................................................................................................*/ public String getAuthors() { return "Peter E. Midford, Ted Garland Jr., and Wayne P. Maddison" ; } /*.................................................................................................................*/ public String getVersion() { return "1.15"; } /*.................................................................................................................*/ public boolean isPrerelease() { return false; } /*................................................................................................................*/ public boolean isSubstantive(){ return true; } /*.................................................................................................................*/ public String getExplanation() { return "Calculates regression passing through a reconstruction of characters at the root."; }} |